Carcinoma diagnosis and treatment, based on odc1 genotype

ABSTRACT

The present invention provides methods and kits a) for predicting colorectal cancer patient survival, as well as the survival of patients harboring other invasive cancers where cellular proliferation and carcinogenesis is linked, in part, to high levels of ODC activity and increased cellular polyamine contents, and b) for selecting the corresponding treatment options for such patients based on the allelic nucleotide sequence or SNP at position +316 of the ODC1 promoter gene as well as cancer treatment methods, in each case, which include the determination of the ODC1 promoter +316 position genotype, as a means to guide treatment selection.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation of U.S. application Ser. No.14/841,750, filed Sep. 1, 2015, which is a continuation of U.S.application Ser. No. 13/709,753, filed Dec. 10, 2012, now U.S. Pat. No.9,121,852, which is a continuation of U.S. application Ser. No.12/780,592, filed May 14, 2010, now U.S. Pat. No. 8,329,636, whichclaims priority to U.S. Provisional Application Nos. 61/217,682, filedJun. 3, 2009, 61/217,679, filed Jun. 3, 2009, and 61/216,216, filed May14, 2009. The entire contents of each of the above-referencedapplications are herein incorporated by reference.

STATEMENT OF FEDERAL FUNDING

This invention was made with government support under grants CA72008(EWG), CA78134 (HAC), CA78285 (HAC), and CA95060 (EWG) from the NationalInstitute of Health, contracts N01-PC-35136, N01-PC-35139 andN01-PC-54404 from the National Cancer Institute and agreement1U58DP00807-01 from the Centers for Disease Control and Prevention. Thegovernment has certain rights in the invention.

INCORPORATION OF SEQUENCE LISTING

The sequence listing that is contained in the file named“CAPPP0006USC3_ST25.txt”, which is 2 KB (as measured in MicrosoftWindows®) and was created on Feb. 21, 2018, is filed herewith byelectronic submission and is incorporated by reference herein.

BACKGROUND OF THE INVENTION I. Field of the Invention

The present invention relates generally to the fields of cancer biologyand medicine. More particularly, it concerns methods for the diagnosis,prevention and treatment of carcinomas and risk factors thereof.

II. Description of Related Art

A major impediment to the translation of cancer chemoprevention researchinto clinical practice has been marginal agent efficacy and toxicitiesthat exceed benefit (Psaty and Potter, 2006; Lippman, 2006). Forexample, the demonstrated marked efficacy of polyamine-inhibitorycombination of long-term daily oral D,L-α-difluoromethylornithine (DFMO,eflornithine) and sulindac among colorectal adenoma (CRA) patients wasrecently demonstrated (Meyskens et al., 2008), however, treatment wasassociated with modest, subclinical ototoxicity (McLaren et al., 2008),and a greater number of cardiovascular events among patients with highbaseline cardiovascular risk (Zell et al., 2009). Identifying geneticfeatures that identify the suitability of a patient for a givenpreventative or curative treatment regime would be a major benefit.

For example, there remains a need for effective and less toxic methodsfor treating and preventing colorectal cancers and other carcinomas.According to the National Cancer Institute, there were approximately147,000 new cases and 50,000 deaths from colorectal cancer in the UnitedStates in 2009. Current treatment protocols, especially those for coloncancers and polyps, include tumor resection, chemotherapy and radiationtherapy. A single nucleotide polymorphism (SNP) in intron-1 of the humanODC1 gene affects ODC1 transcription (Guo et al., 2000), and has beeninvestigated as a genetic marker for colorectal adenoma (CRA) risk(Martinez et al., 2003; Barry et al., 2006; Hubner et al., 2008). Thereported minor A-allele frequency is approximately 25% and despitedifferences across race/ethnicity, ODC1 genotype distribution is inHardy-Weinberg equilibrium within each race (O'Brien et al., 2004; Zellet al., 2009). Individuals homozygous for the ODC1 minor A-allele havereduced risk of adenoma recurrence compared to those with the majorG-allele (Martinez et al., 2003; Hubner et al., 2008). Furthermore, theODC1 A-allele (AA or GA genotype, but not GG genotype) and reportedaspirin usage have been associated with reduced colon polyp recurrence(Martinez et al., 2003; Barry et al., 2006; Hubner et al., 2008), and astatistically significant 50% reduced risk of advanced adenomas (Barryet al., 2006). Whether the ODC1 genotype differentially affects adenomarecurrence, tissue polyamine responses, toxicity profiles and how it maybe used to determine the suitability of preventative and curativetreatments would be a major advantage.

SUMMARY OF THE INVENTION

Thus, in accordance with the present invention, there are providedmethods of treatment, prevention and/or diagnosis related to identifyingpatient's genotype at position +316 of at least one ODC1 promoter geneallele.

In one aspects, there is provided a method for the preventative orcurative treatment of carcinoma in a patient comprising:

-   -   a) obtaining results from a test that determines the patient's        genotype at position +316 of at least one ODC1 promoter gene        allele; and    -   b) if the results indicate that the patient's genotype at        position +316 of at least one allele of the ODC1 promoter gene        is G, administering to the patient effective amounts of a        pharmaceutical therapy comprising:        -   (i) a first agent that inhibits ornithine decarboxylase            (ODC) within the patient; and        -   (ii) a second agent that modulates the polyamine pathway to            reduce overall polyamine content within the patient when            combined with the first agent.

In some embodiments, the second agent also increases the expression ofsperm-idine/spermine N¹-acetyltransferase within the patient. In someembodiments, the results are obtained by receiving a report containingsaid genotype or taking a patient history that reveals the results. Insome embodiments, the test determines the nucleotide base at position+316 of one allele of the ODC1 promoter gene of the patient. In someembodiments, the test determines the nucleotide bases at position +316of both alleles of the ODC1 promoter gene of the patient. In someembodiments, the results indicate that the patient's genotype atposition +316 of both alleles of the ODC1 promoter gene is GG. In someembodiments, the results indicate that the patient's genotype atposition +316 of both alleles of the ODC1 promoter gene is GA.

In some embodiments, the pharmaceutical therapy further comprisesincreasing the dosage of the first or the second agent if the patientwas already being treated with the pharmaceutical therapy, but at alower dosage, prior to obtaining to the results of the test. In someembodiments, the pharmaceutical therapy further comprises increasing thedosage of the first and the second agent if the patient was alreadybeing treated with the pharmaceutical therapy, but at a lower dosage,prior to obtaining to the results of the test. In some embodiments, thefirst agent is α-difluoromethylornithine (DFMO). In some embodiments,the second agent is a non-aspirin containing non-steroidalanti-inflammatory drug (NSAID). In some embodiments, the non-aspirincontaining NSAID is a selective COX-2 inhibitor. In some embodiments,the non-aspirin containing NSAID is sulindac or celecoxib. In someembodiments, the non-aspirin containing NSAID is sulindac.

In another aspect, there is provided a method for the treatment ofcolorectal carcinoma risk factors in a patient comprising:

-   -   a) obtaining results from a test that determines the patient's        genotype at position +316 of at least one ODC1 promoter gene        allele; and    -   b) if the results indicate that the patient's genotype at        position +316 of at least one allele of the ODC1 promoter gene        is G, administering to the patient effective amounts of a        pharmaceutical therapy comprising:        -   (i) a first agent that inhibits ornithine decarboxylase            (ODC) within the patient; and        -   (ii) a second agent that modulates the polyamine pathway to            reduce overall polyamine content within the patient when            combined with the first agent,            wherein the method prevents the formation of new aberrant            crypt foci, new adenomatous polyps or new adenomas with            displasia in the patient.

In some embodiments, the second agent also increases the expression ofspermidine/spermine N¹-acetyltransferase within the patient. In someembodiments, the method prevents the formation of new aberrant cryptfoci in the patient. In some embodiments, the method prevents theformation of new adenomatous polyps in the patient. In some embodiments,the method prevents the formation of new adenomas with displasia in thepatient. In some embodiments, the results are obtained by receiving areport containing said genotype or taking a patient history that revealsthe results. In some embodiments, the test determines the nucleotidebase at position +316 of one allele of the ODC1 promoter gene of thepatient. In some embodiments, the test determines the nucleotide basesat position +316 of both alleles of the ODC1 promoter gene of thepatient. In some embodiments, the results indicate that the patient'sgenotype at position +316 of both alleles of the ODC1 promoter gene isGG. In some embodiments, the results indicate that the patient'sgenotype at position +316 of both alleles of the ODC1 promoter gene isGA.

In some embodiments, the pharmaceutical therapy further comprisesincreasing the dosage of the first or the second agent if the patientwas already being treated with the pharmaceutical therapy, but at alower dosage, prior to obtaining to the results of the test. In someembodiments, the pharmaceutical therapy further comprises increasing thedosage of the first and the second agent if the patient was alreadybeing treated with the pharmaceutical therapy, but at a lower dosage,prior to obtaining to the results of the test. In some embodiments, thefirst agent is α-difluoromethylornithine (DFMO). In some embodiments,the second agent is a non-aspirin containing non-steroidalanti-inflammatory drug (NSAID). In some embodiments, the non-aspirincontaining NSAID is a selective COX-2 inhibitor. In some embodiments,the non-aspirin containing NSAID is sulindac or celecoxib. In someembodiments, the non-aspirin containing NSAID is sulindac.

In another aspect, there is provided a method for evaluating thesuitability of a patient for preventative or curative treatment ofcarcinoma, comprising:

-   -   a) obtaining results from a test that determines the patient's        genotype at position +316 of at least one ODC1 promoter gene        allele; and    -   b) if the results indicate that the patient's genotype at        position +316 of at least one allele of the ODC1 promoter gene        is G, identifying the patient as suitable for treatment by a        pharmaceutical therapy, said therapy comprising combined        effective amounts of a first agent that inhibits ornithine        decarboxylase (ODC) within the patient; and a second agent that        modulates the polyamine pathway to reduce overall polyamine        content within the patient when combined with the first agent.

In some embodiments, the second agent also increases the expression ofsperm-idine/spermine N¹-acetyltransferase within the patient. In someembodiments, the results are obtained by receiving a report containingsaid genotype or taking a patient history that reveals the results. Insome embodiments, the test determines the nucleotide base at position+316 of one allele of the ODC1 promoter gene of the patient. In someembodiments, the test determines the nucleotide bases at position +316of both alleles of the ODC1 promoter gene of the patient. In someembodiments, the results indicate that the patient's genotype atposition +316 of both alleles of the ODC1 promoter gene is GG. In someembodiments, the results indicate that the patient's genotype atposition +316 of both alleles of the ODC1 promoter gene is GA. In someembodiments, the pharmaceutical therapy further comprises increasing thedosage of the first or the second agent if the patient was already beingtreated with the pharmaceutical therapy, but at a lower dosage, prior toobtaining to the results of the test.

In some embodiments, the pharmaceutical therapy further comprisesincreasing the dosage of the first and the second agent if the patientwas already being treated with the pharmaceutical therapy, but at alower dosage, prior to obtaining to the results of the test. In someembodiments, the first agent is α-difluoromethylornithine (DFMO). Insome embodiments, the second agent is a non-aspirin containingnon-steroidal anti-inflammatory drug (NSAID). In some embodiments, thenon-aspirin containing NSAID is a selective COX-2 inhibitor. In someembodiments, the non-aspirin containing NSAID is sulindac or celecoxib.In some embodiments, the non-aspirin containing NSAID is sulindac.

In another aspect, there is provided a method of rendering a carcinomatumor in a patient resectable comprising:

-   -   a) obtaining results from a test that determines the patient's        genotype at position +316 of at least one ODC1 promoter gene        allele; and    -   b) if the results indicate that the patient's genotype at        position +316 of at least one allele of the ODC1 promoter gene        is G, administering to the patient effective amounts of a        pharmaceutical therapy comprising:        -   (i) a first agent that inhibits ornithine decarboxylase            (ODC) within the patient; and        -   (ii) a second agent that increases the expression of            sperm-idine/spermine N¹-acetyltransferase within the            patient.

In some embodiments, the results are obtained by receiving a reportcontaining said genotype or taking a patient history that reveals theresults. In some embodiments, the test determines the nucleotide base atposition +316 of one allele of the ODC1 promoter gene of the patient. Insome embodiments, the test determines the nucleotide bases at position+316 of both alleles of the ODC1 promoter gene of the patient. In someembodiments, the results indicate that the patient's genotype atposition +316 of both alleles of the ODC1 promoter gene is GG. In someembodiments, the results indicate that the patient's genotype atposition +316 of both alleles of the ODC1 promoter gene is GA.

In some embodiments, the pharmaceutical therapy further comprisesincreasing the dosage of the first or the second agent if the patientwas already being treated with the pharmaceutical therapy, but at alower dosage, prior to obtaining to the results of the test. In someembodiments, the pharmaceutical therapy further comprises increasing thedosage of the first and the second agent if the patient was alreadybeing treated with the pharmaceutical therapy, but at a lower dosage,prior to obtaining to the results of the test. In some embodiments, thefirst agent is α-difluoromethylornithine (DFMO).

In some embodiments, the second agent is a non-aspirin containingnon-steroidal anti-inflammatory drug (NSAID). In some embodiments, thenon-aspirin containing NSAID is a selective COX-2 inhibitor. In someembodiments, the non-aspirin containing NSAID is sulindac or celecoxib.In some embodiments, the non-aspirin containing NSAID is sulindac.

In another aspect, there is provided a method for preventing thedevelopment or recurrence of a carcinoma in a patient at risk thereforcomprising:

-   -   a) obtaining results from a test that determines the patient's        genotype at position +316 of at least one ODC1 promoter gene        allele; and    -   b) administering to the patient combined effective amounts of        α-difluoromethylornithine (DFMO) and a non-aspirin containing        non-steroidal anti-inflammatory drug (NSAID) if the results        indicate that the patient's genotype at position +316 of at        least one allele of the ODC1 promoter gene is G.

In some embodiments, the results are obtained by receiving a reportcontaining said genotype or taking a patient history that reveals theresults. In some embodiments, the test determines the nucleotide base atposition +316 of one allele of the ODC1 promoter gene of the patient. Insome embodiments, the test determines the nucleotide bases at position+316 of both alleles of the ODC1 promoter gene of the patient. In someembodiments, the results indicate that the patient's genotype atposition +316 of both alleles of the ODC1 promoter gene is GG. In someembodiments, the results indicate that the patient's genotype atposition +316 of both alleles of the ODC1 promoter gene is GA.

In another aspect, there is provided a method for treating a patient atrisk for development or recurrence of carcinoma withα-difluoromethylornithine (DFMO) and a non-aspirin containingnon-steroidal anti-inflammatory drug (NSAID), comprising administeringto the patient effective amounts of α-difluoromethylornithine (DFMO) anda non-aspirin containing non-steroidal anti-inflammatory drug (NSAID),wherein the patient has been identified as having a G at position +316of at least one ODC1 promoter gene allele.

In some embodiments, the genotype identified at position +316 of both ofthe patient's ODC1 promoter gene alleles is GG. In some embodiments, thegenotype identified at position +316 of both of the patient's ODC1promoter gene alleles is GA.

In another aspect, there is provided a method for treating a carcinomain a patient comprising:

-   -   a) obtaining results from a test that determines the patient's        genotype at position +316 of at least one ODC1 promoter gene        allele; and    -   b) administering to the patient combined effective amounts of        α-difluoromethylornithine (DFMO) and a non-aspirin containing        non-steroidal anti-inflammatory drug (NSAID) if the results        indicate that the patient's genotype at position +316 of the        ODC1 promoter gene of at least one allele is G.

In some embodiments, the results are obtained by receiving a reportcontaining said genotype or taking a patient history that reveals theresults. In some embodiments, the test determines the nucleotide base atposition +316 of one allele of the ODC1 promoter gene of the patient. Insome embodiments, the test determines the nucleotide bases at position+316 of both alleles of the ODC1 promoter gene of the patient. In someembodiments, the results indicate that the patient's genotype atposition +316 of both alleles of the ODC1 promoter gene is GG. In someembodiments, the results indicate that the patient's genotype atposition +316 of both alleles of the ODC1 promoter gene is GA.

In variations on any of the above embodiments, the non-aspirincontaining NSAID is a selective COX-2 inhibitor. In some embodiments,the non-aspirin containing NSAID is sulindac or celecoxib. In someembodiments, the non-aspirin containing NSAID is sulindac. In someembodiments, DFMO and sulindac are administered systemically. In someembodiments, DFMO and sulindac are administered by distinct routes. Insome embodiments, the DFMO or the non-aspirin containing NSAID isadministered orally, intraarterially or intravenously. In someembodiments, the DFMO is administered orally. In some embodiments, theeffective amount of DFMO is 500 mg/day. In some embodiments, the DFMO isadministered intravenously. In some embodiments, the effective amount ofDFMO is from about 0.05 to about 5.0 g/m²/day. In some embodiments, theDFMO and the non-aspirin containing NSAID is formulated for oraladministration. In some embodiments, the DFMO and the non-aspirincontaining NSAID is formulated as a hard or soft capsule or a tablet. Insome embodiments, the DFMO and the non-aspirin containing NSAID isadministered every 12 hours. In some embodiments, the DFMO and thenon-aspirin containing NSAID is administered every 24 hours. In someembodiments, the effective amount of sulindac is from about 10 to about1500 mg/day. In some embodiments, the effective amount of sulindac isfrom about 10 to about 400 mg/day. In some embodiments, the effectiveamount of sulindac is 150 mg/day. In some embodiments, DFMO isadministered prior to sulindac. In some embodiments, DFMO isadministered after sulindac. In some embodiments, DFMO is administeredbefore and after sulindac. In some embodiments, DFMO is administeredconcurrently with sulindac. In some embodiments, DFMO is administered atleast a second time. In some embodiments, sulindac is administered atleast a second time.

In variations on any of the above embodiments, the patient has a solidtumor, and said method further comprises resection of said solid tumor.In some embodiments, DFMO and sulindac are administered prior to saidresection. In some embodiments, DFMO and sulindac are administered aftersaid resection.

In variations on any of the above embodiments, the carcinoma iscolorectal cancer, breast cancer, pancreatic cancer, brain cancer, lungcancer, stomach cancer, a blood cancer, skin cancer, testicular cancer,prostate cancer, ovarian cancer, liver cancer or esophageal cancer,cervical cancer, head and neck cancer, non-melanoma skin cancer,neuroblastoma and glioblastoma. In some embodiments, the carcinoma iscolorectal cancer. In some embodiments, the colorectal cancer is stageI. In some embodiments, the colorectal cancer is stage II. In someembodiments, the colorectal cancer is stage III. In some embodiments,the colorectal cancer is stage IV.

In variations on any of the above embodiments, the method prevents theformation of new advanced colorectal neoplasms within the patient. Insome embodiments, the method prevents ototoxicity or the risk thereofwithin the patient. In some embodiments, the method prevents theformation of new right-sided advanced colorectal neoplasms. In someembodiments, the method prevents the formation of new left-sidedadvanced colorectal neoplasms.

In variations on any of the above embodiments, the patient has beenidentified as having one or more adenomatous polyps in the colon, rectumor appendix. In some embodiments, the patient has been identified ashaving one or more advanced colorectal neoplasms. In some embodiments,the patient has been identified as having one or more left-side advancedcolorectal neoplasms. In some embodiments, the patient has beenidentified as having one or more right-sided advanced colorectalneoplasms. In some embodiments, the patient has been diagnosed withfamilial adenomatous polyposis. In some embodiments, the patient hasbeen diagnosed with Lynch syndrome. In some embodiments, the patient hasbeen diagnosed with familial colorectal cancer type X. In someembodiments, the patient satisfies the Amsterdam Criteria or theAmsterdam Criteria II. In some embodiments, the patient has a history ofresection of one or more colorectal adenomas. In some embodiments, thepatient has an intraepithelial neoplasia or a precancerous lesionassociated ODC hyperactivity. In some embodiments, the patient has anintraepithelial neoplasia or a precancerous lesion and elevated cellularpolyamine levels.

In variations on any of the above embodiments, the patient is human.

The use of the word “a” or “an,” when used in conjunction with the term“comprising” in the claims and/or the specification may mean “one,” butit is also consistent with the meaning of “one or more,” “at least one,”and “one or more than one.”

Throughout this application, the term “about” is used to indicate that avalue includes the inherent variation of error for the device, themethod being employed to determine the value, or the variation thatexists among the study subjects.

The terms “comprise,” “have” and “include” are open-ended linking verbs.Any forms or tenses of one or more of these verbs, such as “comprises,”“comprising,” “has,” “having,” “includes” and “including,” are alsoopen-ended. For example, any method that “comprises,” “has” or“includes” one or more steps is not limited to possessing only those oneor more steps and also covers other unlisted steps.

The term “effective,” as that term is used in the specification and/orclaims, means adequate to accomplish a desired, expected, or intendedresult.

As used herein, the term “IC₅₀” refers to an inhibitory dose which is50% of the maximum response obtained.

As used herein, the term “patient” or “subject” refers to a livingmammalian organism, such as a human, monkey, cow, sheep, goat, dog, cat,mouse, rat, guinea pig, or transgenic species thereof. In certainembodiments, the patient or subject is a primate. Non-limiting examplesof human subjects are adults, juveniles, infants and fetuses.

“Pharmaceutically acceptable” means that which is useful in preparing apharmaceutical composition that is generally safe, non-toxic and neitherbiologically nor otherwise undesirable and includes that which isacceptable for veterinary use as well as human pharmaceutical use.

“Prevention” or “preventing” includes: (1) inhibiting the onset of adisease in a subject or patient which may be at risk and/or predisposedto the disease but does not yet experience or display any or all of thepathology or symptomatology of the disease, and/or (2) slowing the onsetof the pathology or symptomatology of a disease in a subject or patientwhich may be at risk and/or predisposed to the disease but does not yetexperience or display any or all of the pathology or symptomatology ofthe disease.

“Effective amount,” “Therapeutically effective amount” or“pharmaceutically effective amount” means that amount which, whenadministered to a subject or patient for treating a disease, issufficient to effect such treatment for the disease.

“Treatment” or “treating” includes (1) inhibiting a disease in a subjector patient experiencing or displaying the pathology or symptomatology ofthe disease (e.g., arresting further development of the pathology and/orsymptomatology), (2) ameliorating a disease in a subject or patient thatis experiencing or displaying the pathology or symptomatology of thedisease (e.g., reversing the pathology and/or symptomatology), and/or(3) effecting any measurable decrease in a disease in a subject orpatient that is experiencing or displaying the pathology orsymptomatology of the disease.

The above definitions supersede any conflicting definition in any of thereference that is incorporated by reference herein. The fact thatcertain terms are defined, however, should not be considered asindicative that any term that is undefined is indefinite. Rather, allterms used are believed to describe the invention in terms such that oneof ordinary skill can appreciate the scope and practice the presentinvention.

Other objects, features and advantages of the present disclosure willbecome apparent from the following detailed description. It should beunderstood, however, that the detailed description and the specificexamples, while indicating specific embodiments of the invention, aregiven by way of illustration only, since various changes andmodifications within the spirit and scope of the invention will becomeapparent to those skilled in the art from this detailed description.Note that simply because a particular compound is ascribed to oneparticular generic formula doesn't mean that it cannot also belong toanother generic formula.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and areincluded to further demonstrate certain aspects of the presentdisclosure. The invention may be better understood by reference to oneof these drawings in combination with the detailed description ofspecific embodiments presented herein.

FIG. 1—Differential Effects of Polyamine Regulation by MAD1 and c-MYC.Schema depicting the proposed differential effects of polyamineregulation by MAD1 and c-MYC on the ODC1+316 minor A-allele. Effects ofthe ODC inhibitor DFMO (difluoromethylornithine) are also shown.

FIG. 2—Colorectal Cancer-Specific Survival Rate Estimates. This figureshows Kaplan-Meier colorectal cancer-specific survival rate estimatesfor cases with stage III colorectal cancer, stratified by ODC1+316genotype. Included are cases from the University of California IrvineGene-Environment Study of Familial Colorectal Cancer diagnosed duringthe period 1994-1996 with follow-up through March 2008: ODC1 GG (64cases, 15 colorectal cancer-specific deaths), ODC1 GA/AA (62 cases, 25colorectal cancer-specific deaths).

FIGS. 3A & B—Location and Analysis of the ODC1 promoter SNP. FIG. Ashows the A, location of the ODC1 promoter SNP. The SNP underinvestigation in this study is 316 nucleotides 3′ of the ODC1transcription start site (*). This SNP resides between two consensusE-boxes as shown by the underlined sequences, and affects a PstIrestriction site (box) (SEQ ID NO:5). FIG. 3B shows a restrictionfragment length polymorphism analysis of ODC1 SNP. The DNA was obtainedfrom two cell types, and the region surrounding the ODC1 SNP site wassequenced. Colon-derived HT29 cells were found to be heterozygous GA,whereas HCT116 cells were found to be homozygous GG, at the ODC1 SNPlocus. A 350-bp PCR product of this region was obtained from each celltype and subjected to digestion with PstI. Evidence of an A-allele wasindicated by restriction products <350 bp.

FIGS. 4A & B—E-Box Expression and Immunoprecipitation Analysis. Locationof the ODC1 promoter SNP. FIG. 4A shows E-box protein expression incolon-derived cells. Expression of proteins to be evaluated for bindingto the +316 ODC1 SNP was assessed by Western blot analysis. Extracts ofboth HT29 and HCT116 cells were evaluated for c-MYC, MAD1, and MAD4;(3-actin was used as a loading control. FIG. 4B shows documentation forthe allele-specific transcription factor binding by chromatinimmunoprecipitation analysis, which was conducted as described in theexamples section below. HT29 cells were a source of ODC1 A-alleles, asthese cells are heterozygous GA at this site. HCT116 cells were used asa source of ODC1 G-alleles.

FIGS. 5A & B—Effects of c-MYC and MAD1 expression on ODC1 Activity. FIG.5A shows the effect of c-MYC expression on ODC1 allele-specific promoteractivity in HT29 colon-derived cells. Promoter activity was measuredafter transfection with ODC1 promoter reporter plasmids co-transfectedwith pcDNA 3.0 plasmid or CMV-MYC expression vector. Promoter constructsdiffer by the presence of the first E-box element, located in −485 to−480 bp (“wt E-box1” for the wild-type sequence or “mut E-box1” for amutant sequence). The constructs differ also by the ODC1 +316 SNP (“+316G” or “+316 A”). *, P≤0.013 for each of the four comparisons relative topromoter activity with pcDNA 3.0 cotransfection. FIG. 5B shows theeffect of MAD1 expression on ODC1 allele-specific promoter activity inHT29 colon tumor derived cells. Promoter activity was measured aftertransfection with ODC1 promoter reporter plasmids cotransfected withpcDNA 3.1 plasmid or with a pcDNA-MAD/plasmid. Promoter constructs usedwere described in the legend for panel A of this figure. *, P=0.027,statistical significance relative to promoter activity with pcDNA 3.1cotransfection.

FIG. 6—Reduction in Adenomatous Polyps. This figure shows the percentrecurrence of adenomatous polyps of patients were treated with DFMO andSulindac compared with placebo. There was a 70% reduction in totaladenoma, a 92% reduction in advanced adenoma, and 95% reduction inmultiple adenoma.

FIG. 7—Pharmacogenomic Benefit/Risk Analysis Based on +316 ODC1Genotype. This figure compares reduction in % recurrence of adenomas atthe end of 3 years versus placebo, with % ototoxicity for treatment andplacebo groups as a function of the patient's+316 ODC1 genotype.Ototoxicity was determined using audiometric testing.

FIG. 8A-C—Pharmacogenomic Benefit/Risk Analysis Based on +316 ODC1Genotype. This figure compares benefit, reduction in % recurrence ofadenomas at the end of 3 years, with risk, % ototoxicity, for treatmentand placebo groups as a function of the patient's +316 ODC1 genotype.Ototoxicity was determined using audiometric testing.

FIG. 9—Average Number of Tumors by Size in Colon of Min/+ Mice. Thisfigure shows the average number of tumors by size in the colon of thethree treatment groups compared to untreated controls. Mice, purchasedfrom The Jackson Laboratory (Bar Harbor, Me.), were bred crossingC57BL/6J-Apc^(Min/+) males and C57/BL6 females. Heterozygous Min mice(Apc^(Min)/Apc⁺): (heterozygous for a nonsense mutation at codon 850 ofApc) were identified by genotyping at weaning by an allele specific PCRassay using tail-tip DNA. Homozygous (Apc⁺/Apc⁺) litter mates served ascontrols. One treatment consisted of supplementing drinking water with2% DFMO (Merrell Dow Research Inst.) on the 8th day of study. In theother treatment, 167 ppm of sulindac (Harlen Teklad) was added toAIN-93G mouse diet on the 21st day of the study. The third treatment wasa combination of DFMO and sulindac. After 114 days, the mice weresacrificed through CO₂ asphyxiation. The small intestine and colonsegments were removed from mice and dissected lengthwise, mounted andfixed in 70% ethanol, and placed at 4° C. for tumor scoring.Representative tissues were also taken for histopathology evaluation.

FIG. 10—Average Number of Tumors by Size in the Small Intestine of Min/+Mice. This figure shows the average number of tumors by size in thesmall intestine of the three treatment groups compared to untreatedcontrols. For experimental details, see FIG. 9 description above.

FIG. 11—Number of High Grade Adenomas as a Function of Therapy in Min/+Mice. This figure shows how the number of high grade adenomas variousdepending on therapy type. For experimental details, see FIG. 9description above.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

In several aspects, methods are provided that comprise predicting thesuitability, efficacy, toxicity and/or dosage of anti-carcinomacombination therapies comprising ornithine decarboxylase (ODC) inhibitorand a spermidine/spermine N¹-acetyltransferase expression agonist basedat least in part on the patient's ODC1 promoter genotype.

The present invention also involves the delivery of therapeuticcompounds to individuals exhibiting pre-cancerous symptoms to preventthe onset of cancer and/or to prevent the onset of cancer risk factors,such as the formation of new aberrant crypt foci, the formation of newadenomatous polyps or new adenomas with dysplasia. Cells of thiscategory include polyps and other precancerous lesions, premalignancies,preneoplastic or other aberrant phenotype indicating probableprogression to a cancerous state, based at least in part on thepatient's ODC1 promoter genotype.

I. POLYAMINES METABOLISM

Excess polyamine formation has long been implicated in epithelialcarcinogenesis, particularly colorectal carcinogenesis. Polyamines aresmall ubiquitous molecules involved in various processes, includingtranscription, RNA stabilization, ion channel gating and others(Wallace, 2000). Ornithine decarboxylase (ODC), the first enzyme inpolyamine synthesis, is essential for normal development and tissuerepair in mammals but is down-regulated in most adult tissues (Gernerand Meyskens, 2004). Multiple abnormalities in the control of polyaminemetabolism and transport result in increased polyamine levels that canpromote tumorigenesis in several tissues (Thomas and Thomas, 2003).

Polyamine metabolism is up-regulated in intestinal epithelial tissues ofhumans with familial adenomatous polyposis (FAP) (Giardiello et al.,1997), a syndrome associated with high risk of colon and other cancers.

FAP may be caused by mutations in the adenomatous polyposis coli (APC)tumor suppressor gene, and APC signaling has been shown regulates ODCexpression in both human cells (Fultz and Gerner, 2002) and in a mousemodel of FAP (Erdman et al., 1999).

Wild type APC expression leads to decreased expression of ODC, whilemutant APC leads to increased expression of ODC. The mechanism ofAPC-dependent regulation of ODC involves E-box transcription factors,including the transcriptional activator c-MYC and the transcriptionalrepressor MAD1 (Fultz and Gerner, 2002; Martinez et al., 2003). c-MYCwas shown by others to regulate ODC transcription (Bellofernandez etal., 1993). Several genes involved in polyamine metabolism are essentialgenes for optimal growth in most organisms, and are down-regulated innon-proliferating and/or adult cells and tissues (Gerner and Meyskens,2004). The polyamines influence specific cellular phenotypes, in part,by affecting patterns of gene expression, as reviewed elsewhere (Childset al., 2003).

As described below, a strategy involving inhibition of ODC activity(i.e., the rate-limiting enzyme of polyamine synthesis) and/or reductionof cellular polyamine levels has demonstrated remarkable efficacy inpreventing recurrence of colorectal polyps in humans. Epidemiologic andexperimental results from the present research demonstrate conditionalregulation of polyamine homeostasis by genetic polymorphism in ODC, andsuggest a model in which the +316 ODC SNP may be protective for colonadenoma recurrence and detrimental for survival after colon cancerdiagnosis. This information may be used for determining colon cancerprognosis. By identifying patients at increased risk for cancerprogression/recurrence, early implementation of tertiary preventionmanagement strategies can be instituted. Additionally, this research maybe used to identify high-risk but otherwise optimally-treatedlocoregional colorectal cancer patients that would benefit from tertiarycancer prevention therapies.

Depending on a patient's diet, the excess polyamine problem may becompounded by the fact that polyamines, e.g., putrescine is present inmany common foods, such as orange juice, which contains approximately400 ppm putrescine. In this regard, a high polyamine diet iscontraindicatory, and for some of the embodiments provided herein such adiet is to be avoided. See U.S. Provisional patent application byKavitha P. Raj, Jason A. Zell, Christine E. McLaren, Eugene W. Gerner,Frank L. Meyskens and Jeffrey Jacob, entitled “Cancer Prevention andTreatment Methods Based on Dietary Polyamine Content,” filed May 14,2010, which is incorporated by reference in its entirety.

II. FAMILIAL ADENOMATOUS POLYPOSIS

Familial Adenomatous Polyposis (FAP), an inherited polyposis syndrome,is the result of germ-line mutation of the adenomatous polyposis coli(APC) tumor suppressor gene (Su et al., 1992). This autosomal-dominantcondition with variable expression is associated with the development ofhundreds of colonic adenomas, which uniformly progress to adenocarcinomaby forty years of age, two decades earlier than the mean age diagnosisfor sporadic colon cancer (Bussey, 1990). In prior studies ofpre-symptomatic individuals with FAP, increased levels of the polyaminesspermidine and spermine, and their diamine precursor putrescine, havebeen detected in normal-appearing colorectal biopsies when compared tonormal family member controls (Giardiello et al., 1997). The activity ofornithine decarboxylase (ODC), the first and rate-limiting enzyme inmammalian polyamine synthesis, also is elevated in apparently normalcolonic mucosal biopsies from FAP patients (Giardiello et al., 1997; Lukand Baylin, 1984). These findings are of interest as the polyamines arenecessary for optimal cell proliferation (Pegg, 1986). Further,suppression of ODC activity, using the enzyme-activated irreversibleinhibitor DFMO, inhibits colon carcinogenesis in carcinogen-treatedrodents (Kingsnorth et al., 1983; Tempero et al., 1989).

As discussed in greater detail below, the Min (multiple intestinalneoplasia) mouse, which shares a mutated APC/apc genotype with FAP,serves as a useful experimental animal model for human FAP patients(Lipkin, 1997). The Min mouse can develop greater than 100gastrointestinal adenomas/adenocarcinomas throughout thegastrointestinal tract by 120 days of life leading to GI bleeding,obstruction and death. A combination therapy of DFMO and sulindac wasshown to be effective in reducing adenomas in these mice (U.S. Pat. No.6,258,845; Gerner and Meyskens, 2004). The results of treating Min micewith either DFMO alone, sulindac alone, or a combination of DFMO andsulindac on tumor formation in either the colon or small intestine areshown in FIGS. 9-11.

III. ORNITHINE DECARBOXYLASE-1 POLYMORPHISM

Activity of ornithine decarboxylase (ODC), the first enzyme in polyaminesynthesis, is required for normal growth and is elevated in manycancers, including colorectal cancer. Herein associations of the +316ODC single nucleotide polymorphism (SNP) with colorectal cancer(CRC)-specific survival among CRC cases were examined and its functionalsignificance in colon cancer cells was investigated.

A single nucleotide polymorphism (SNP) in intron-1 of the human ODC1gene affects ODC1 transcription (Guo et al., 2000), and has beeninvestigated as a genetic marker for colorectal adenoma (CRA) risk(Martinez et al., 2003; Barry et al., 2006; Hubner et al., 2008). Thereported minor A-allele frequency is approximately 25% and despitedifferences across race/ethnicity, ODC1 genotype distribution is inHardy-Weinberg equilibrium within each race (O'Brien et al., 2004; Zellet al., 2009). Individuals homozygous for the ODC1 minor A-allele havereduced risk of adenoma recurrence compared to those with the majorG-allele (Martinez et al., 2003; Hubner et al., 2008). Furthermore, theODC1 A-allele (AA or GA genotype, but not GG genotype) and reportedaspirin usage have been associated with reduced colon polyp recurrence(Martinez et al., 2003; Barry et al., 2006; Hubner et al., 2008), and astatistically significant 50% reduced risk of advanced adenomas (Barryet al., 2006).

The ODC allele-specific binding of E-box transcription factors wasinvestigated and the functional significance of the +316 ODC SNP,located between two E-boxes was evaluated (E-box 2 and 3 as depicted inFIG. 2A). Each cell line genotype influences a consensus PstIrestriction site in this region. FIG. 2B shows that a polymerase chainreaction (PCR) product made from human colon HT29 cells was partiallysensitive to PstI cutting, suggesting that these cells contained atleast one ODC A-allele. A PCR product made from human colon HCT116 cellsusing the same primers was insensitive to PstI action, implying thatthese cells contained only ODC G-alleles. This result was confirmed bydirect DNA sequencing.

Expression of specific E-box binding proteins, including thetranscriptional activator c-MYC and several transcriptional repressorsin HT29 and HCT116 cells (e.g. MAD1 and MAD4), was established byWestern blotting (FIG. 3A). Chromatin immunoprecipitation (CHIP)analysis of the region surrounding +316 of the ODC promoter wasconducted, using antibodies directed against these proteins. As shown inFIG. 3B, ODC promoter-specific PCR products were synthesized from HT29DNA obtained after immunoprecipitation of chromatin with antibodiesdirected against c-MYC, MAD1 or MAD4. PCR products synthesized fromHCT116 DNA after similar chromatin immunoprecipitation weresubstantially reduced compared to those synthesized from HT29 DNA.Quantification of these results indicated that c-MYC, MAD1, and MAD4binding to the ODC SNP region was 4-14 times greater in HT29 cells,which contained one ODC-A allele, compared to HCT116 cells, whichcontained only ODC-G alleles.

ODC allele-specific promoter activity was assessed. The hypothesis that+316 ODC SNP influenced ODC expression in a manner dependant on theexpression of E-box activators and repressors was tested as follows.Transient co-transfection of colon cancer-derived HT29 cells wasaccomplished with ODC allele-specific promoter constructs in combinationwith vectors expressing either the transcriptional activator c-MYC orthe repressor MAD1 (FIGS. 4A & B). The standard error bars shown reflectthe variability in triplicate measurements within a singlerepresentative experiment, which has been replicated. Theallele-specific promoter-reporters used in these experiments includedall three E-boxes shown in FIG. 2A. As shown in FIG. 4A, c-MYCexpression had the greatest stimulatory effect on promoters containingthree consensus E-boxes and the ODC-A allele (wt E-box1 +316 A,P=0.0014). Deletion of the upstream E-box reduced promoter activity, butc-MYC expression continued to stimulate this activity (mut E-box1 +316A, P=0.0013). Substitution of a G for the A at the +316 SNP positionreduced the ability of c-MYC to stimulate promoter activity even with anintact 5′ flanking consensus E-box. Mutation of the 5′ flankingconsensus E-box in combination with the ODC-G allele further reducedpromoter activity.

When MAD1, rather than c-MYC, was co-transfected with the ODCallele-specific promoter reporters (FIG. 4B), the repressor was onlyable to reduce the activity of the ODC promoter which contained allthree E-boxes and the wild-type +316 A-allele (P=0.027). Deletion of theupstream E-box (mut E-box 1 +316A) significantly reduced the effect ofMAD1 on ODC promoter activity. Substitution of G for A at the +316position rendered promoters containing either two or three E-boxesunresponsive to MAD1 suppression.

IV. DIFLUOROMETHYLORNITHINE (DFMO)

DFMO, also know as eflornithine, has the following chemical designation;2-(difluoromethyl)-dl-ornithine. It is an enzyme-activated irreversibleinhibitor of ornithine decarboxylase (ODC), the rate limiting enzyme ofthe polyamine biosynthetic pathway. As a result of this inhibition ofpolyamine synthesis, the compound is effective in preventing cancerformation in many organ systems, inhibiting cancer growth, and reducingtumor size. It also has synergistic action with other antineoplasticagents.

DFMO has been shown to decrease APC-dependent intestinal tumorigenesisin mice (Erdman et al., 1999). Oral DFMO administered daily to humansinhibits ODC enzyme activity and polyamine contents in a number ofepithelial tissues (Love et al., 1993; Gerner et al., 1994; Meyskens etal., 1994; Meyskens et al., 1998; Simoneau et al., 2001; Simoneau etal., 2008). Recently, the inventors reported that DFMO in combinationwith the non-steroidal anti-inflammatory drug (NSAID) sulindac, has beenreported to markedly lower the adenoma recurrence rate among individualswith colonic adenomas when compared to placebos in a randomized clinicaltrial (Meyskens et al., 2008).

DFMO was originally synthesized by Centre de Recherche Merrell,Strasbourg; Current FDA approvals include

-   -   African sleeping sickness. High dose systemic IV dosage form—not        marketed (Sanofi/WHO)    -   Hirsutis (androgen-induced excess hair growth) topical dosage        form No oral formulations are currently approved.

DFMO and its use in the treatment of benign prostatic hypertrophy aredescribed in two patents, U.S. Pat. Nos. 4,413,141, and 4,330,559. U.S.Pat. No. 4,413,141 describes DFMO as being a powerful inhibitor of ODC,both in vitro and in vivo. Administration of DFMO causes a decrease inputrescine and spermidine concentrations in cells in which thesepolyamines are normally actively produced. Additionally, DFMO has beenshown to be capable of slowing neoplastic cell proliferation when testedin standard tumor models. U.S. Pat. No. 4,330,559 describes the use ofDFMO and DFMO derivatives for the treatment of benign prostatichypertrophy. Benign prostatic hypertrophy, like many disease statescharacterized by rapid cell proliferation, is accompanied by abnormalelevation of polyamine concentrations. The treatment described withinthis reference can be administered to a patient either orally, orparenterally.

DFMO can potentially be given continuously with significant anti-tumoreffects. This drug is relatively non-toxic at low doses of 0.4 g/m²/dayto humans while producing inhibition of putrescine synthesis in tumors.Studies in a rat-tumor model demonstrate that DFMO infusion can producea 90% decrease in tumor putrescine levels without suppressing peripheralplatelet counts.

Side effects observed with DFMO include effects on hearing at high dosesof 4 g/M²/day that resolve when it is discontinued. These effects onhearing are not observed at lower doses of 0.4 g/M²/day whenadministered for up to one year (Meyskens et al., 1994). In addition afew cases of dizziness/vertigo are seen that resolve when the drug isstopped. Thrombocytopenia has been reported predominantly in studiesusing high “therapeutic” doses of DFMO (>1.0 g/m²/day) and primarily incancer patients who had previously undergone chemotherapy or patientswith compromised bone marrow. Although the toxicity associated with DFMOtherapy are not, in general, as severe as other types of chemotherapy,in limited clinical trials it has been found to promote a dose-relatedthrombocytopenia. Moreover, studies in rats have shown that continuousinfusion of DFMO for 12 days significantly reduces platelet countscompared with controls. Other investigations have made similarobservations in which thrombocytopenia is the major toxicity ofcontinuous i.v. DFMO therapy. These findings suggest that DFMO maysignificantly inhibit ODC activity of the bone marrow precursors ofmegakaryocytes. DFMO may inhibit proliferative repair processes, such asepithelial wound healing.

A phase III clinical trial assessed the recurrence of adenomatous polypsafter treatment for 36 months with difluoromethylornithine (DFMO) plussulindac or matched placebos. Temporary hearing loss is a known toxicityof treatment with DFMO, thus a comprehensive approach was developed toanalyze serial air conduction audiograms. The generalized estimatingequation method estimated the mean difference between treatment armswith regard to change in air conduction pure tone thresholds whileaccounting for within-subject correlation due to repeated measurementsat frequencies. Based on 290 subjects, there was an average differenceof 0.50 dB between subjects treated with DFMO plus sulindac comparedwith those treated with placebo (95% confidence interval, −0.64 to 1.63dB; P=0.39), adjusted for baseline values, age, and frequencies. In thenormal speech range of 500 to 3,000 Hz, an estimated difference of 0.99dB (−0.17 to 2.14 dB; P=0.09) was detected. Dose intensity did not addinformation to models. There were 14 of 151 (9.3%) in the DFMO plussulindac group and 4 of 139 (2.9%) in the placebo group who experiencedat least 15 dB hearing reduction from baseline in 2 or more consecutivefrequencies across the entire range tested (P=0.02). Follow-up airconduction done at least 6 months after end of treatment showed anadjusted mean difference in hearing thresholds of 1.08 dB (−0.81 to 2.96dB; P=0.26) between treatment arms. There was no significant differencein the proportion of subjects in the DFMO plus sulindac group whoexperienced clinically significant hearing loss compared with theplacebo group. The estimated attributable risk of ototoxicity fromexposure to the drug is 8.4% (95% confidence interval, −2.0% to 18.8%;P=0.12). There is a <2 dB difference in mean threshold for patientstreated with DFMO plus sulindac compared with those treated withplacebo. The results of this study are discussed in greater detail inMcLaren et al., 2008, which is incorporated herein by reference in itsentirety. Provided herein are methods of reducing and/or preventingototoxicity in patients treated with agents such as DFMO and sulindac.

V. NSAIDS

NSAIDs are anti-inflammatory agents that are not steroids. In additionto anti-inflammatory actions, they have analgesic, antipyretic, andplatelet-inhibitory actions. They are used primarily in the treatment ofchronic arthritic conditions and certain soft tissue disordersassociated with pain and inflammation. They act by blocking thesynthesis of prostaglandins by inhibiting cyclooxygenase, which convertsarachidonic acid to cyclic endoperoxides, precursors of prostaglandins.Inhibition of prostaglandin synthesis accounts for their analgesic,antipyretic, and platelet-inhibitory actions; other mechanisms maycontribute to their anti-inflammatory effects. Certain NSAIDs also mayinhibit lipoxygenase enzymes or phospholipase C or may modulate T-cellfunction. (AMA Drug Evaluations Annual, 1814-5, 1994).

The nonsteroidal anti-inflammatory drugs (NSAIDs), including aspirin,ibuprofen, piroxicam (Reddy et al., 1990; Singh et al., 1994),indomethacin (Narisawa, 1981), and sulindac (Piazza et al., 1997; Rao etal., 1995), effectively inhibit colon carcinogenesis in the AOM-treatedrat model. NSAIDs also inhibit the development of tumors harboring anactivated Ki-ras (Singh and Reddy, 1995). NSAIDs appear to inhibitcarcinogenesis via the induction of apoptosis in tumor cells (Bedi etal., 1995; Lupulescu, 1996; Piazza et al., 1995; Piazza et al., 1997b).A number of studies suggest that the chemopreventive properties of theNSAIDs, including the induction of apoptosis, is a function of theirability to inhibit prostaglandin synthesis (reviewed in DuBois et al.,1996; Lupulescu, 1996; Vane and Botting, 1997). Studies, however,indicate that NSAIDs may act through both prostaglandin-dependent and-independent mechanisms (Alberts et al., 1995; Piazza et al., 1997a;Thompson et al., 1995; Hanif, 1996). Sulindac sulfone, a metabolite ofthe NSAID sulindac, lacks COX-inhibitory activity yet induces apoptosisin tumor cells (Piazza et al., 1995; Piazza et al., 1997b) and inhibitstumor development in several rodent models of carcinogenesis (Thompsonet al., 1995; Piazza et al., 1995, 1997a).

Several NSAIDs have been examined for their effects in human clinicaltrials. A phase IIa trial (one month) of ibuprofen was completed andeven at the dose of 300 mg/day, a significant decrease in prostoglandinE₂ (PGE₂) levels in flat mucosa was seen. A dose of 300 mg of ibuprofenis very low (therapeutic doses range from 1200-3000 mg/day or more), andtoxicity is unlikely to be seen, even over the long-term. However, inanimal chemoprevention models, ibuprofen is less effective than otherNSAIDs.

A. Sulindac and its Major Metabolites, Sulindac Sulfone and SulindacSulfide

Sulindac is a non-steroidal, anti-inflammatory indene derivative withthe following chemical designation; (Z)-5-fluoro-2-methyl-1-((4(methylsulfin-yl)phenyl)methylene) 1H-indene-3-acetic acid (Physician'sDesk Reference, 1999). The sulfinyl moiety is converted in vivo byreversible reduction to a sulfide metabolite and by irreversibleoxidation to a sulfone metabolite (exisulind). See U.S. Pat. No.6,258,845, which is incorporated herein by reference in its entirety.Sulindac, which also inhibits Ki-ras activation, is metabolized to twodifferent molecules which differ in their ability to inhibit COX, yetboth are able to exert chemopreventive effects via the induction ofapoptosis. Sulindac sulfone lacks COX-inhibitory activity, and mostlikely facilitates the induction of apoptosis in a manner independent ofprostaglandin synthesis. Available evidence indicates that the sulfidederivative is at least one of the biologically active compounds. Basedon this, sulindac may be considered a prodrug.

Sulindac (Clinoril®) is available, for example, as 150 mg and 200 mgtablets. The most common dosage for adults is 150 to 200 mg twice a day,with a maximal daily dose of 400 mg. After oral administration, about90% of the drug is absorbed. Peak plasma levels are achieved in about 2hours in fasting patients and 3 to 4 hours when administered with food.The mean half-life of sulindac is 7.8 hours: the mean half-life of thesulfide metabolite is 16.4 hours. U.S. Pat. Nos. 3,647,858 and 3,654,349cover preparations of sulindac, both are incorporate by reference hereinin their entireties.

Sulindac is indicated for the acute and long-term relief of signs andsymptoms of osteoarthritis, rheumatoid arthritis, ankylosingspondylitis, acute gout, and acute painful shoulder. The analgesic andantiinflammatory effects exerted by sulindac (400 mg per day) arecomparable to those achieved by aspirin (4 g per day), ibuprofen (1200mg per day), indometacin (125 mg per day), and phenylbutazone (400 to600 mg per day). Side effects of sulindac include mild gastrointestinaleffects in nearly 20% of patients, with abdominal pain and nausea beingthe most frequent complaints. CNS side effects are seen in up to 10% ofpatients, with drowsiness, headache, and nervousness being those mostfrequently reported. Skin rash and pruritus occur in 5% of patients.Chronic treatment with sulindac can lead to serious gastrointestinaltoxicity such as bleeding, ulceration, and perforation.

The potential use of sulindac for chemoprevention of cancers, and inparticular colorectal polyps, has been well studied. Two recent U.S.Pat. Nos. 5,814,625 and 5,843,929, detail potential chemopreventive usesof sulindac in humans. Both patents are incorporated herein in theirentireties. Doses of sulindac claimed in U.S. Pat. No. 5,814,625 rangefrom 10 mg to 1500 mg per day, with preferred doses of 50 mg to 500 mgper day. However, at the higher doses, the biggest problem with the useof sulindac as a single agent in chemoprevention is its well-knowntoxicities and moderately high risk of intolerance. The elderly appearto be especially vulnerable, as the incidence of side effects is higherin those over the age of 60. It is noted that this age group is mostlikely to develop colorectal cancer, and therefore, most likely tobenefit from chemoprevention.

Sulindac and its sulfone metabolite exisulind have been tested andcontinue to be tested clinically for the prevention and treatment ofseveral cancer types. Clinical Trials.gov, a U.S. National Institutes ofHealth database provides the following overview of as of May 10, 2010.

Status Clinical Trial Recruiting A Randomized Study of Sulindac in OralPremalignant Lesions Conditions: Leukoplakia, Oral; Benign NeoplasmsInterventions: Drug: sulindac; Drug: Placebo Sponsors: MemorialSloan-Kettering Cancer Center; Head and Neck Surgery, AIMS, Cochin,India; Weill Medical College of Cornell University; Regional CancerCentre (RCC), Trivandrum, India; Mazumdar Shaw Cancer Center (MSCC)Phase: Not listed Recruiting Sulindac in Preventing Melanoma in HealthyParticipants Who Are at Increased Risk of Melanoma Condition:Precancerous Condition Interventions: Drug: sulindac; Other: placeboSponsors: University of Arizona; National Cancer Institute (NCI) Phase:Phase II Active, not Eflornithine and Sulindac in Preventing ColorectalCancer in Patients recruiting With Colon Polyps Conditions: ColorectalCancer; Precancerous/Nonmalignant Condition Intervention: Drug:eflornithine plus sulindac Sponsors: University of California, Irvine;Chao Family Comprehensive Cancer Center; National Cancer Institute (NCI)Phase: Phase III Completed Sulindac in Preventing Breast Cancer in Womenat High Risk for Breast Cancer Condition: Breast Cancer Interventions:Drug: sulindac; Other: laboratory biomarker analysis Sponsors:University of Arizona; National Cancer Institute (NCI) Phase: Phase ICompleted Sulindac Capsules Compared With Sulindac Tablets in HealthyVolunteers Condition: Unspecified Adult Solid Tumor, Protocol SpecificInterventions: Drug: sulindac; Other: pharmacological study Sponsors:Mayo Clinic; National Cancer Institute (NCI) Phase: Active, notEflornithine Plus Sulindac in Preventing Colorectal Cancer in Patientsrecruiting With Benign Colorectal Polyps Condition: Colorectal CancerIntervention: Drug: eflornithine plus sulindac Sponsors: University ofCalifornia, Irvine; Chao Family Comprehensive Cancer Center; NationalCancer Institute (NCI) Phase: Phase II Active, not Bevacizumab/Tarcevaand Tarceva/Sulindac in Squamous Cell recruiting Carcinoma of the Headand Neck Condition: Squamous Cell Carcinoma of the Head and Neck (SCCHN)Interventions: Drug: Bevacizumab; Drug: erlotinib; Drug: SulindacSponsors: Massachusetts General Hospital; Dana- Farber Cancer Institute;Emory University; University of North Carolina, Chapel Hill; Genentech;OSI Pharmaceuticals Phase: Phase II Active, not Sulindac in PreventingLung Cancer in Current or Former Smokers With recruiting BronchialDysplasia Conditions: Lung Cancer; Precancerous Condition; Tobacco UseDisorder Interventions: Drug: sulindac; Other: placebo Sponsors: MayoClinic; National Cancer Institute (NCI) Phase: Phase II CompletedSulindac and Tamoxifen in Treating Patients With Desmoid TumorCondition: Desmoid Tumor Interventions: Drug: sulindac; Drug: tamoxifencitrate Sponsors: Children's Oncology Group; National Cancer Institute(NCI) Phase: Phase II Recruiting Sulindac and Epirubicin in TreatingPatients With Metastatic Malignant Melanoma Condition: Melanoma (Skin)Interventions: Drug: epirubicin hydrochloride; Drug: sulindac; Other:immunologic technique Sponsor: All Ireland Cooperative Oncology ResearchGroup Phase: Phase II Completed Atorvastatin, Oligofructose-EnrichedInulin, or Sulindac in Preventing Cancer in Patients at Increased Riskof Developing Colorectal Neoplasia Conditions: Colorectal Cancer;Precancerous Condition Interventions: Dietary Supplement: oligofructose-enriched inulin; Drug: atorvastatin calcium; Drug: sulindac; Other:placebo Sponsors: Mayo Clinic; National Cancer Institute (NCI) Phase:Phase II Suspended Sulindac and Plant Compounds in Preventing ColonCancer Condition: Colorectal Cancer Interventions: Dietary Supplement:curcumin; Dietary Supplement: rutin; Drug: quercetin; Drug: sulindacSponsor: Rockefeller University Phase: Active, not Comparison ofSulindac, Aspirin, and Ursodiol in Preventing Colorectal recruitingCancer Condition: Colorectal Cancer Interventions: Drug: acetylsalicylicacid; Drug: sulindac; Drug: ursodiol Sponsors: M.D. Anderson CancerCenter; National Cancer Institute (NCI) Phase: Phase II CompletedSulindac and Docetaxel in Treating Women With Metastatic or RecurrentBreast Cancer Condition: Breast Cancer Interventions: Drug: docetaxel;Drug: sulindac Sponsors: Fox Chase Cancer Center; National CancerInstitute (NCI) Phase: Phase II Recruiting Influence of Sulindac andProbiotics on the Development of Pouch Adenomas in Patients WithFamilial Adenomatous Polyposis Condition: Adenomatous Polyposis ColiInterventions: Drug: Sulindac (drug); Drug: VSL#3 (probiotic); Drug:Inulin (probiotic) Sponsors: Radboud University; Dutch Cancer SocietyPhase: Phase II Terminated The Effects of Curcuminoids on Aberrant CryptFoci in the Human Colon Condition: Aberrant Crypt Foci Interventions:Drug: sulindac; Drug: curcumin Sponsor: University of Medicine andDentistry New Jersey Phase: Recruiting Use of Curcumin for Treatment ofIntestinal Adenomas in Familial Adenomatous Polyposis (FAP) Conditions:Lower Tract Polyps in Patients With FAP; Upper Tract Polyps in PatientsWith FAP Interventions: Drug: Calcumin (Curcumin); Other: Risk FactorQuestionnaire; Other: Blood samples; Other: Biopsies (Sigmoidoscopy);Other: Biopsies (Upper endoscopy) Sponsor: University of Puerto RicoPhase: Active, not To Lengthen the Duration of the Off-Treatment ofIntermittent Androgen recruiting Suppression Condition: Prostate CancerInterventions: Drug: Flutamide; Drug: Leuprolide Acetate; Drug:Exisulind Sponsors: University of Washington; OSI Pharmaceuticals Phase:Phase II Completed Safety, Efficacy and Pharmacokinetic BetweenCapecitabine and Exisulind in Metastatic Breast Cancer PatientsConditions: Breast Neoplasms; Metastases, Neoplasm Interventions: Drug:Capecitabine; Drug: Exisulind Sponsors: M.D. Anderson Cancer Center;Cell Pathways Phases: Phase I/Phase II Completed Neoadjuvant Exisulindin Treating Patients Who Are Undergoing Radical Prostatectomy for StageII or Stage III Prostate Cancer Condition: Prostate CancerInterventions: Drug: exisulind; Procedure: conventional surgery;Procedure: neoadjuvant therapy Sponsors: Mayo Clinic; National CancerInstitute (NCI) Phase: Phase II Completed Combination Chemotherapy inTreating Patients With Advanced Non- Small Cell Lung Cancer Condition:Lung Cancer Interventions: Drug: carboplatin; Drug: exisulind; Drug:gemcitabine hydrochloride Sponsors: Eastern Cooperative Oncology Group;National Cancer Institute (NCI) Phase: Phase II Completed Phase II Studyof Taxotere in Combination With Exisulind in Non-Small Cell Lung Cancer(NSCLC) Patients Condition: NSCLC Intervention: Drug: Exisulind Sponsor:OSI Pharmaceuticals Phases: Phase I/Phase II Completed A Phase III Studyof the Efficacy of Taxotere/Aptosyn Versus Taxotere/Placebo in Non-SmallCell Lung Cancer Patients Condition: Non-Small Cell Lung CancerIntervention: Drug: Exisulind Sponsor: OSI Pharmaceuticals Phase: PhaseIII Completed Exisulind Versus Placebo After Surgical Removal of theProstate Condition: Prostatic Neoplasms Intervention: Drug: ExisulindSponsors: Mayo Clinic; OSI Pharmaceuticals Phase: Phase II CompletedDocetaxel, Estramustine, and Exisulind in Treating Patients WithMetastatic Prostate Cancer That Has Not Responded to Hormone TherapyCondition: Prostate Cancer Interventions: Drug: docetaxel; Drug:estramustine phosphate sodium; Drug: exisulind Sponsors: Cancer andLeukemia Group B; National Cancer Institute (NCI) Phase: Phase IICompleted Combination Chemotherapy and Exisulind in Treating PatientsWith Extensive-Stage Small Cell Lung Cancer Condition: Lung CancerInterventions: Drug: carboplatin; Drug: etoposide; Drug: exisulindSponsors: Cancer and Leukemia Group B; National Cancer Institute (NCI)Phase: Phase II Active, not Exisulind in Preventing Polyps in PatientsWith Familial Adenomatous recruiting Polyposis Conditions: ColorectalCancer; Small Intestine Cancer Intervention: Drug: exisulind Sponsor:University of Utah Phases: Phase II/Phase III Completed Exisulind Priorto Radical Prostatectomy Condition: Prostatic Neoplasms Intervention:Drug: Exisulind Therapy Sponsors: Mayo Clinic; National Cancer Institute(NCI) Phase: Phase II

B. Piroxicam

A non-steroidal anti-inflammatory agent that is well established in thetreatment of rheumatoid arthritis and osteoarthritis with the followingchemical designation;4-hydroxy-2-methyl-N-2-pyridyl-2H-1,2-benzothiazine-3-carboxamide1,1-dioxide. Its usefulness also has been demonstrated in the treatmentof musculoskeletal disorders, dysmenorrhea, and postoperative pain. Itslong half-life enables it to be administered once daily. The drug hasbeen shown to be effective if administered rectally. Gastrointestinalcomplaints are the most frequently reported side effects.

Piroxicam has been shown to be effective chemoprevention agent in animalmodels (Pollard and Luckert, 1989; Reddy et al., 1987), although itdemonstrated side effects in a recent IIb trial. A large meta-analysisof the side effects of the NSAIDs also indicates that piroxicam has moreside effects than other NSAIDs (Lanza et al., 1995). Sulindac has beenshown to produce regression of adenomas in Familial AdenomatousPolyposis (FAP) patients (Muscat et al., 1994), although at least onestudy in sporadic adenomas has shown no such effect (Ladenheim et al.,1995).

The combination of DFMO and piroxicam has been shown to have asynergistic chemopreventive effect in the AOM-treated rat model of coloncarcinogenesis (Reddy et al., 1990), although DFMO exerted a greatersuppressive effect than piroxicam on Ki-ras mutation and tumorigenesiswhen each agent was administered separately (Reddy et al., 1990). In onestudy, administration of DFMO or piroxicam to AOM-treated rats reducedthe number of tumors harboring Ki-ras mutations from 90% to 36% and 25%respectively (Singh et al., 1994). Both agents also reduced the amountof biochemically active p21 ras in existing tumors.

C. Combinations of NSAIDs

Combinations of various NSAIDs are also used for various purposes. Byusing lower doses of two or more NSAIDs, it is possible to reduce theside effects or toxicities associated with higher doses of individualNSAIDs. For example, in some embodiments, sulindac may be used togetherwith celecoxib. In some embodiments, the one or both of the NSAIDS areselective COX-2 inhibitors. Examples of NSAIDS that back be used eitheralone or in combination include, but are not limited to, the following:ibuprofen, naproxen, fenoprofen, ketoprofen, flurbiprofen, oxaprozin,indomethacin, sulindac, etodolac, diclofenac, piroxicam, meloxicam,tenoxicam, droxicam, lornoxicam, isoxicam, mefenamic acid, meclofenamicacid, flufenamic acid, tolfenamic acid, celecoxib rofecoxib valdecoxibparecoxib, lumiracoxib, or etoricoxib.

VI. EFLORNITHINE/SULINDAC COMBINATION THERAPY

Preclinical studies of chemoprevention drugs given in combination at lowdoses show remarkable efficacy in preventing adenomas with littleadditional toxicities, suggesting a strategy to improve risk to benefitratios for preventing recurrent adenomas.

As noted above, the Min (multiple intestinal neoplasia) mouse, whichshares a mutated APC/apc genotype with FAP, serves as a usefulexperimental animal model for human FAP patients (Lipkin, 1997). The Minmouse can develop greater than 100 gastrointestinaladenomas/adenocarcinomas throughout the gastrointestinal tract by 120days of life leading to GI bleeding, obstruction and death. Acombination therapy of DFMO and sulindac was shown to be effective inreducing adenomas in these mice (U.S. Pat. No. 6,258,845; Gerner andMeyskens, 2004). The results of treating Min mice with either DFMOalone, sulindac alone, or a combination of DFMO and sulindac on tumorformation in either the colon or small intestine are shown in FIGS. 9 &10. FIG. 9 shows the average number of tumors by size in the colon ofthe three treatment groups compared to untreated controls. FIG. 10 showsthe average number of tumors by size in the small intestine of the threetreatment groups compared to untreated controls. FIG. 11 shows how thenumber of high grade adenomas various depending on therapy, single orcombination.

VII. EFFICACY OF POLYAMINE-INHIBITORY THERAPY BASED ON PATIENT PROFILE

The efficacy of a polyamine-inhibitory combination of long-term dailyoral D,L-α-difluoromethylornithine (DFMO, eflornithine) and sulindacamong CRA patients was demonstrated (Meyskens et al., 2008), however,treatment was associated with modest, subclinical ototoxicity (McLarenet al., 2008), and a greater number of cardiovascular events amongpatients with high baseline cardiovascular risk (Zell et al., 2009). Theinventors have now investigated determined that the ODC1 genotypedifferentially affects adenoma recurrence, tissue polyamine responses,or toxicity profiles after eflornithine and sulindac treatment comparedto placebo.

Three hundred seventy-five patients with history of resected (> or =3mm) adenomas were randomly assigned to receive oraldifluoromethylornithine (DFMO) 500 mg and sulindac 150 mg once daily ormatched placebos for 36 months, stratified by use of low-dose aspirin(81 mg) at baseline and clinical site. Follow-up colonoscopy was done 3years after randomization or off-study. Colorectal adenoma recurrencewas compared among the groups with log-binomial regression. Comparingthe outcome in patients receiving placebos to those receiving activeintervention, (a) the recurrence of one or more adenomas was 41.1% and12.3% (risk ratio, 0.30; 95% confidence interval, 0.18-0.49; P<0.001);(b) 8.5% had one or more advanced adenomas, compared with 0.7% ofpatients (risk ratio, 0.085; 95% confidence interval, 0.011-0.65;P<0.001); and (c) 17 (13.2%) patients had multiple adenomas (>1) at thefinal colonoscopy, compared with 1 (0.7%; risk ratio, 0.055;0.0074-0.41; P<0.001). Serious adverse events (grade> or =3) occurred in8.2% of patients in the placebo group, compared with 11% in the activeintervention group (P=0.35). There was no significant difference in theproportion of patients reporting hearing changes from baseline.Recurrent adenomatous polyps can be markedly reduced by a combination oflow oral doses of DFMO and sulindac and with few side effects. Thedetails of this study are discussed in greater detail below and inMeyskens et al., 2008, which is incorporated herein by reference in itsentirety.

The study was halted by the Data Safety Monitoring Board (DSMB) after267 patients completed end-of-study colonoscopies (due to the studymeeting its efficacy endpoints). The DSMB monitored all safety andefficacy endpoints. As discussed in greater detail in the Examples,section this study involves analysis of patient data from themulticenter phase III colon adenoma prevention trial. See also (Meyskenset al., 2008), which is incorporated herein by reference in itsentirety.

A. ODC1 Genotype Distribution

A total of 440 colorectal cancer (CRC) cases identified from the UCIrvine CRC gene-environment study were used in the case-only analysis.Median follow-up duration was 11 years. There were 270 (61%) coloncancer cases, 162 (37%) rectal cancer cases, and 8 (2%) CRC cases ofunspecified location. Clinicopathologic data for colon and rectal cancercases are shown in Table 1. ODC +316 genotype distribution among all CRCcases was 53% GG, 41% GA, and 7% AA. ODC +316 genotype distribution wassimilar among CRC cases with and without a family history. There were nosignificant differences in ODC genotype distribution by age (P=0.38),gender (P=0.56), family history (P=0.94), site within the colorectum(P=0.55), histology (P=0.46) or tumor grade (P=0.73). ODC genotypedistribution did not significantly differ by stage at diagnosis: stage I(49% GG, 42% GA, 8% AA), stage II (56% GG, 38% GA, 6% AA), stage III(51% GG, 43% GA, 6% AA), stage IV (59% GG, 37% GA, 4% AA) (P=0.87). ODCgenotype distribution by ethnicity revealed significant differences:Caucasian (382 cases: 53% GG, 41% GA, 6% AA, minor-A allelefrequency=26%), African-American (7 cases: 71% GG, 29% GA, 0% AA,minor-A allele frequency=15%), Hispanics (21 cases: 57% GG, 43% GA, 0%AA, minor-A allele frequency=21%), and Asians (27 cases: 33% GG, 41% GA,26% AA, minor-A allele frequency=46%) (P=0.009). However, within eachrace ODC genotype distribution was in Hardy-Weinberg equilibrium(Caucasians P=0.36, African-Americans P=0.66, Hispanics P=0.21, AsiansP=0.35).

B. Adenoma Recurrence

ODC1 genotype distribution was: 126 GG (55%), 87 GA (38%), and 15 AA(7%). Baseline clinical characteristics revealed differences, as shownin Table 1. In regression models with predictors age, gender, race,aspirin use, treatment, ODC1 genotype, and treatment, treatment was theonly factor associated with differences in adenoma recurrence, tissuepolyamine response, and ototoxicity. A statistically significantinteraction was detected for ODC1 genotype and treatment in the fullmodel for adenoma recurrence (P=0.021), such that the pattern of adenomarecurrence among placebo patients was: GG-50%, GA-35%, AA-29% versuseflornithine/sulindac patients: GG-11%, GA-14%, AA-57%.

A statistically significant interaction was detected between ODC1genotype and treatment in this model (P=0.038). ODC1 genotype was notsignificantly associated with a tissue putrescine response orspermidine:spermine ratio response in the full regression models (datanot shown). The relative risk (RR) for adenoma recurrence related totreatment after adjustment in the full regression model was 0.39 (95% CI0.24-0.66). There were no significant associations between treatment andODC1 genotype group with regard to cardiovascular or gastrointestinaladverse events (Tables 3 & 4).

Here it was observed that the adenoma-inhibitory effect of eflornithineand sulindac was greater among those with the major G homozygous ODC1genotype, in contrast to prior reports showing decreased risk ofrecurrent adenoma among CRA patients receiving aspirin carrying at leastone A-allele (Martinez et al., 2003; Barry et al., 2006; Hubner et al.,2008) ODC1 genotype distribution was similar to that reported in prioraspirin-based trials (Martinez et al., 2003; Barry et al., 2006; Hubneret al., 2008), and the A-allele was associated with a non-significantlower recurrent adenoma risk in the placebo group consistent withprevious reports (Martinez et al., 2003; Hubner et al., 2008). Theseresults demonstrate that ODC1 A-allele carriers differ in response toprolonged exposure with eflornithine and sulindac compared to GGgenotype patients, with A-allele carriers experiencing less benefit interms of adenoma recurrence, and potential for elevated risk ofdeveloping ototoxicity, especially among the AA homozygotes.

C. Survival Analysis

Of the 440 CRC cases, 138 (31%) were deceased at the time of analysis.Sixty-four (46%) deaths occurred in cases carrying the GG genotype,compared to 74 (54%) deaths in cases with the AA/AG genotypes. Cause ofdeath was available for 102 of the 138 deceased CRC cases. Eighty-five(83%) CRC cases died as a result of CRC. A statistically significantimprovement in CRC-specific survival was observed among all CRC caseshomozygous for the ODC G-allele (10-year survival=84%) compared to caseswith at least one A-allele (ODC GA/AA) (10-year survival=76%; P=0.031).CRC-specific survival analysis by stage revealed that significantlydifferent survival differences were not observed for AJCC stage I(P=0.055), II (P=0.61), or IV (P=0.65) CRC. However, among cases withstage III CRC the ODC GG genotype was associated with improved 10-yearCRC-specific survival: 75% compared to 60% for ODC GA/AA genotype cases;P=0.024 (FIG. 1). Among colon cancer cases, a statistically significantCRC-specific survival benefit was observed for those with ODC GGgenotype compared to ODC GA/AA cases (10-year survival rate=87% vs. 79%;P=0.029); this was not observed for rectal cancer cases (10-yearsurvival=78% for ODC GG cases vs. 72% for ODC GA/AA cases; P=0.42).

Among all CRC cases, the CRC-specific survival estimates based on ODCgenotype after adjustment for age (years), gender, ethnicity, familyhistory of CRC, TNM stage at diagnosis, tumor site within the colon,histologic subtype, treatment with surgery, radiation therapy, andchemotherapy were a follows: ODC GG hazards ratio (HR)=1.00 (referent),ODC GA HR=1.73, and ODC AA genotype HR=1.73 (P-trend=0.0283). Amongcolon cases only, CRC-specific survival analysis revealed that the ODC+316 SNP was an independent predictor of CRC-specific survival, afteradjustment for the above clinical variables. Compared to ODC GG coloncancer cases, the CRC-specific risk of death (HR) was 2.31 (1.15-4.64)for ODC GA genotype and 3.73 (0.93-14.99) for ODC AA genotype(P-trend=0.006) (Table 2). Overall survival analysis of these coloncancer cases was consistent with the CRC-specific survival analysis(Table 2). Among rectal cancer cases, CRC-specific survival analysisrevealed that the ODC +316 SNP was not an independent predictor ofCRC-specific survival after adjustment for the aforementioned clinicalvariables. Compared to ODC GG rectal cancer cases (HR=1.00, reference),the CRC-specific risk of death (HR) was 1.72 (0.83-3.57) for ODC GAheterozygotes and 1.93 (0.56-6.67) for ODC AA homozygotes(P-trend=0.12).

As noted above, the ODC +316 genotype distribution differed acrossethnicity. The observed mortality risk, other than by chance, likelyreflects differences based on ODC genotype, however the risk may berestricted to a particular ethnic group. Thus multivariate analyses wereconducted among Caucasian colon cancer cases, to assessgenotype-specific mortality risk within this single ethnic group. Amongthe 234 Caucasian colon cancer cases, there were 37 CRC-related deaths.Multivariate CRC-specific survival analysis revealed that the ODC +316SNP was an independent predictor of CRC-specific survival amongCaucasian colon cancer cases after adjustment for the aforementionedrelevant clinical variables. Compared to cases with ODC GG genotype(HR=1.00, reference), the CRC-specific risk of death (HR) was 2.67(1.22-5.82) for ODC GA genotype and 6.28 (1.46-26.95) for ODC AAgenotype (P-trend=0.0018).

Genotype-specific survival differences among CRC cases were limited tocolon cancer cases: compared to ODC GG genotype cases (HR=1.00,reference) the adjusted CRC-SS hazards ratio (HR) was 2.31 (1.15-4.64)for ODC GA cases and 3.73 (0.93-14.99) for ODC AA cases (P-trend=0.006).In colon cancer cells, the ODC +316 SNP, flanked by two E-boxes,predicts ODC promoter activity. The E-box activator c-MYC and repressorsMAD1 and MAD4 preferentially bind to minor A−, compared to major G−,alleles in cultured cells.

Based on this population-based analysis of colorectal cancer cases witheleven years follow-up duration, it was observed that the +316 ODC SNPwas associated with colorectal cancer specific survival among coloncancer cases. A statistically significant increased risk of CRC-specificmortality was observed with each additional ODC A-allele among coloncancer cases, i.e., from ODC GG to GA to AA (P-trend=0.006), afteradjustment for age, gender, ethnicity, tumor stage, family history ofCRC, tumor site, histology, treatment with surgery, radiation therapy,and chemotherapy.

D. Allele Specific Regulation of Transcription Factors

The experimental data presented here provide insights into potentialbiologic mechanisms underlying our clinical observations. In coloncancer epithelial cells, we have shown that the ODC +316 SNP isfunctionally significant, as evidenced by increased binding of E-boxtranscription factors to promoter elements containing A−, compared toG−, alleles. Both the activator c-MYC and the repressor MAD1 showgreater effects on promoter activity in reporter elements containing A−versus G− alleles. These results suggest allele-specific regulation ofODC by E-box transcription factors. ODC protein enzyme activity is notapparently affected by the ODC +316 SNP genotype, which we believeinfluences ODC transcription.

In colon cells, it has been shown that conditional expression of wildtype APC, a gene expressed in normal colonic mucosa, suppresses c-MYC,and increases MAD1, expression (Fultz and Gerner, 2002). Further, it hashave reported that wild type APC can regulate ODC promoter activity in amanner dependent on the +316 SNP (Martinez et al., 2003). Wild type APCis expressed in the apparently normal colonic mucosa of individuals notafflicted with FAP, while the majority of sporadic colon adenomas showevidence of mutated or deleted APC (Iwamoto et al., 2000). MYC isexpressed at low levels in normal intestinal mucosa but is increased inintestinal adenomas of APC^(Min/+) mice. Conditional knockout ofintestinal epithelial MYC expression suppresses intestinal tumorigenesisin APC^(Min/+) mice (Ignatenko et al., 2006). As described above,previous work by our group (Martinez et al., 2003) and others (Hubner etal., 2008) demonstrated a protective role for the ODC A-allele,especially in aspirin users, against recurrence of colon polyps inclinical prevention trials. However, in the population-based studypresented here, the ODC A-allele was associated with poor survival. Thisapparent contradiction may be explained by the results shown here, whichindicate that both E-box activators and repressors bind the ODC A-alleleselectively. The inventors speculate that the transition from normalepithelium, expressing E-box repressors, to neoplastic epithelium may beretarded in individuals with ODC A-alleles. This effect may result fromsuppression of polyamine synthesis. However, if the transformedepithelium begins to express E-box activators (such as c-MYC), thencancer progression may be more likely to occur in individuals with theODC A genotype. Our results for risk of colon cancer-specific mortalityare consistent with those of others showing that risk of prostate cancermay be associated with the ODC A-allele among specific individuals asthe result of gene environment interactions (O'Brien et al., 2004;Visvanathan et al., 2004). Such colon cancer progression could be due toenhanced polyamine synthesis, as has been demonstrated already forprostate cancer (Simoneau et al., 2008).

This finding that a factor, such as the ODC SNP, may have both promotingand inhibiting effects on carcinogenesis is not unique. For example,transforming growth factor-beta (TGF-β) has diverse roles incarcinogenesis and cancer progression (Derynck et al., 2001; Pardali andMoustakas, 2007; Roberts and Wakefield, 2003). TGF-β in untransformedcells inhibits cell proliferation and induces apoptosis. Yet, it isoverexpressed in all human tumors and is associated with late cancerprogression, specifically tumor invasion and metastasis. A single studyreporting ODC activity in human colorectal tumors demonstrated that highlevels of ODC expression was significantly associated with improvedsurvival (Matsubara et al., 1995). This suggests that, although ODCoverexpression promotes the formation of human colorectal adenomas, itis possible that in established lesions, ODC overexpression causesenhanced proliferation and is associated with improved response toanti-proliferative treatments. However, that study did not includestratification by ODC genotype, so it is not known if these effects areindependent of ODC genotype.

The observed associations of the ODC +316 SNP with CRC-specificmortality were limited to colon cancer cases. Among colon cancer cases,particularly strong effects were observed for Caucasians. Similar toother reports, the ODC +316 SNP allele frequency differs considerably byethnicity (O'Brien et al., 2004). When the inventors limited thesurvival analysis to Caucasians only (i.e., the only ethnic group withadequate power for such analyses), the associations of the ODC +316 SNPwere significant, and of greater magnitude than the estimates observedfor the entire cohort.

The epidemiologic study shares limitations of other population-basedanalyses, including lack of data on comorbid conditions, performancestatus, and particular chemotherapeutic regimens utilized. Additionally,the tissue biopsy samples obtained from participants of the UC IrvineGene-Environment Study of Familial Colorectal Cancer areparaffin-embedded specimens and therefore cannot be used for accurateassessment of tissue polyamine quantification by high performance liquidchromatography (HPLC). There is also the potential for selection bias,favoring a relatively healthy group of CRC survivors, since there was amedian 16 month delay from the time of CRC diagnosis until studyenrollment. Other factors affecting polyamine metabolism that were notaccounted for in the present study may explain our observations. Forexample, aspirin activates polyamine acetylation and export and workswith the ODC A-allele to reduce cell and tissue polyamine contents(Gerner et al., 2004; Martinez et al., 2003; Babbar et al., 2006).

In summary, the inventors have observed clinical consequences of the ODC+316 SNP on CRC-specific mortality among colon cancer cases.Additionally, the inventors have further established the functionalsignificance of the ODC +316 SNP in the c-MYC- and MAD1-dependenttranscription of this gene in human colon cancer cells. Together, theseexperimental and epidemiologic findings suggest roles for the ODC +316SNP in progression of colon cancer that are distinct from its previouslyreported role in progression to colon adenomas. These findings may beused to assess risk of colon cancer progression and may be used todirect patient-specific pharmacogenetic management, surveillancemonitoring, and inform novel targeted approaches to secondary andtertiary colon cancer prevention.

E. Summary

A statistically significant interaction was detected for ODC1 genotypeand treatment in the full model for adenoma recurrence (P=0.021), suchthat the pattern of adenoma recurrence among placebo patients was:GG-50%, GA-35%, AA-29% versus eflornithine/sulindac patients: GG-11%,GA-14%, AA-57%. Here it was observed that the adenoma-inhibitory effectof eflornithine and sulindac was greater among those with the major Ghomozygous ODC1 genotype, in contrast to prior reports showing decreasedrisk of recurrent adenoma among CRA patients receiving aspirin carryingat least one A-allele (Martinez et al., 2003; Barry et al., 2006; Hubneret al., 2008) These results demonstrate that ODC1 A-allele carriersdiffer in response to prolonged exposure with eflornithine and sulindaccompared to GG genotype patients, with A-allele carriers experiencingless benefit in terms of adenoma recurrence, and potential for elevatedrisk of developing ototoxicity, especially among the AA homozygotes.

VIII. POLYMORPHISM ANALYSIS

The genotype at the +316 position of the ODC1 promoter gene of patientcan determined using the methods provided below, including the specificmethods described in the Examples section. These methods can be furthermodified and optimized using the principles and techniques of molecularbiology as applied by a person skilled in the art. Such principles andtechniques are taught, for example, in Small et al., (2002), which isincorporated herein by reference. General methods employed for theidentification of single nucleotide polymorphisms (SNPs) are providedbelow. The reference of Kwok and Chen (2003) and Kwok (2001) provideoverviews of some of these methods; both of these references arespecifically incorporated by reference.

SNPs relating to ODC1 can be characterized by the use of any of thesemethods or suitable modification thereof. Such methods include thedirect or indirect sequencing of the site, the use of restrictionenzymes where the respective alleles of the site create or destroy arestriction site, the use of allele-specific hybridization probes, theuse of antibodies that are specific for the proteins encoded by thedifferent alleles of the polymorphism, or any other biochemicalinterpretation.

A. DNA Sequencing

A commonly used method of characterizing a polymorphism is direct DNAsequencing of the genetic locus that flanks and includes thepolymorphism. Such analysis can be accomplished using either the“dideoxy-mediated chain termination method,” also known as the “SangerMethod” (Sanger et al., 1975) or the “chemical degradation method,” alsoknown as the “Maxam-Gilbert method” (Maxam et al., 1977). Sequencing incombination with genomic sequence-specific amplification technologies,such as the polymerase chain reaction may be utilized to facilitate therecovery of the desired genes (Mullis et al., 1986; European PatentApplication 50,424; European Patent Application. 84,796, European PatentApplication 258,017, European Patent Application. 237,362; EuropeanPatent Application. 201,184; U.S. Pat. Nos. 4,683,202; 4,582,788; and4,683,194), all of the above incorporated herein by reference.

B. Exonuclease Resistance

Other methods that can be employed to determine the identity of anucleotide present at a polymorphic site utilize a specializedexonuclease-resistant nucleotide derivative (U.S. Pat. No. 4,656,127). Aprimer complementary to an allelic sequence immediately 3′—to thepolymorphic site is hybridized to the DNA under investigation. If thepolymorphic site on the DNA contains a nucleotide that is complementaryto the particular exonucleotide-resistant nucleotide derivative present,then that derivative will be incorporated by a polymerase onto the endof the hybridized primer. Such incorporation makes the primer resistantto exonuclease cleavage and thereby permits its detection. As theidentity of the exonucleotide-resistant derivative is known one candetermine the specific nucleotide present in the polymorphic site of theDNA.

C. Microsequencing Methods

Several other primer-guided nucleotide incorporation procedures forassaying polymorphic sites in DNA have been described (Komher et al.,1989; Sokolov, 1990; Syvanen 1990; Kuppuswamy et al., 1991; Prezant etal., 1992; Ugozzoll et al., 1992; Nyren et al., 1993). These methodsrely on the incorporation of labeled deoxynucleotides to discriminatebetween bases at a polymorphic site. As the signal is proportional tothe number of deoxynucleotides incorporated, polymorphisms that occur inruns of the same nucleotide result in a signal that is proportional tothe length of the run (Syvanen et al., 1990).

D. Extension in Solution

French Patent 2,650,840 and PCT Application WO91/02087 discuss asolution-based method for determining the identity of the nucleotide ofa polymorphic site. According to these methods, a primer complementaryto allelic sequences immediately 3′—to a polymorphic site is used. Theidentity of the nucleotide of that site is determined using labeleddideoxynucleotide derivatives which are incorporated at the end of theprimer if complementary to the nucleotide of the polymorphic site.

E. Genetic Bit Analysis or Solid-Phase Extension

PCT Application WO92/15712 describes a method that uses mixtures oflabeled terminators and a primer that is complementary to the sequence3′ to a polymorphic site. The labeled terminator that is incorporated iscomplementary to the nucleotide present in the polymorphic site of thetarget molecule being evaluated and is thus identified. Here the primeror the target molecule is immobilized to a solid phase.

F. Oligonucleotide Ligation Assay (OLA)

This is another solid phase method that uses different methodology(Landegren et al., 1988). Two oligonucleotides, capable of hybridizingto abutting sequences of a single strand of a target DNA are used. Oneof these oligonucleotides is biotinylated while the other is detectablylabeled. If the precise complementary sequence is found in a targetmolecule, the oligonucleotides will hybridize such that their terminiabut, and create a ligation substrate. Ligation permits the recovery ofthe labeled oligonucleotide by using avidin. Other nucleic aciddetection assays, based on this method, combined with PCR have also beendescribed (Nickerson et al., 1990). Here PCR is used to achieve theexponential amplification of target DNA, which is then detected usingthe OLA.

G. Ligase/Polymerase-Mediated Genetic Bit Analysis

U.S. Pat. No. 5,952,174 describes a method that also involves twoprimers capable of hybridizing to abutting sequences of a targetmolecule. The hybridized product is formed on a solid support to whichthe target is immobilized. Here the hybridization occurs such that theprimers are separated from one another by a space of a singlenucleotide. Incubating this hybridized product in the presence of apolymerase, a ligase, and a nucleoside triphosphate mixture containingat least one deoxynucleoside triphosphate allows the ligation of anypair of abutting hybridized oligonucleotides. Addition of a ligaseresults in two events required to generate a signal, extension andligation. This provides a higher specificity and lower “noise” thanmethods using either extension or ligation alone and unlike thepolymerase-based assays, this method enhances the specificity of thepolymerase step by combining it with a second hybridization and aligation step for a signal to be attached to the solid phase.

H. Invasive Cleavage Reactions

Invasive cleavage reactions can be used to evaluate cellular DNA for aparticular polymorphism. A technology called INVADER® employs suchreactions (e.g., de Arruda et al., 2002; Stevens et al., 2003, which areincorporated by reference). Generally, there are three nucleic acidmolecules: 1) an oligonucleotide upstream of the target site (“upstreamoligo”), 2) a probe oligonucleotide covering the target site (“probe”),and 3) a single-stranded DNA with the target site (“target”). Theupstream oligo and probe do not overlap but they contain contiguoussequences. The probe contains a donor fluorophore, such as fluoroscein,and an acceptor dye, such as Dabcyl. The nucleotide at the 3′ terminalend of the upstream oligo overlaps (“invades”) the first base pair of aprobe-target duplex. Then the probe is cleaved by a structure-specific5′ nuclease causing separation of the fluorophore/quencher pair, whichincreases the amount of fluorescence that can be detected. See Lu etal., 2004.

In some cases, the assay is conducted on a solid-surface or in an arrayformat.

I. Other Methods to Detect SNPs

Several other specific methods for polymorphism detection andidentification are presented below and may be used as such or withsuitable modifications in conjunction with identifying polymorphisms ofthe ODC1 gene in the present invention. Several other methods are alsodescribed on the SNP web site of the NCBI on the World Wide Web atncbi.nlm.nih.gov/SNP, incorporated herein by reference.

In a particular embodiment, extended haplotypes may be determined at anygiven locus in a population, which allows one to identify exactly whichSNPs will be redundant and which will be essential in associationstudies. The latter is referred to as ‘haplotype tag SNPs (htSNPs)’,markers that capture the haplotypes of a gene or a region of linkagedisequilibrium. See Johnson et al. (2001) and Ke and Cardon (2003), eachof which is incorporated herein by reference, for exemplary methods.

The VDA-assay utilizes PCR amplification of genomic segments by long PCRmethods using TaKaRa LA Taq reagents and other standard reactionconditions. The long amplification can amplify DNA sizes of about2,000-12,000 bp. Hybridization of products to variant detector array(VDA) can be performed by a Affymetrix High Throughput Screening Centerand analyzed with computerized software.

A method called Chip Assay uses PCR amplification of genomic segments bystandard or long PCR protocols. Hybridization products are analyzed byVDA, Halushka et al. (1999), incorporated herein by reference. SNPs aregenerally classified as “Certain” or “Likely” based on computer analysisof hybridization patterns. By comparison to alternative detectionmethods such as nucleotide sequencing, “Certain” SNPs have beenconfirmed 100% of the time; and “Likely” SNPs have been confirmed 73% ofthe time by this method.

Other methods simply involve PCR amplification following digestion withthe relevant restriction enzyme. Yet others involve sequencing ofpurified PCR products from known genomic regions.

In yet another method, individual exons or overlapping fragments oflarge exons are PCR-amplified. Primers are designed from published ordatabase sequences and PCR-amplification of genomic DNA is performedusing the following conditions: 200 ng DNA template, 0.5 μM each primer,8004 each of dCTP, dATP, dTTP and dGTP, 5% formamide, 1.5 mM MgCl₂, 0.5U of Taq polymerase and 0.1 volume of the Taq buffer. Thermal cycling isperformed and resulting PCR-products are analyzed by PCR-single strandconformation polymorphism (PCR-SSCP) analysis, under a variety ofconditions, e.g, 5 or 10% polyacrylamide gel with 15% urea, with orwithout 5% glycerol. Electrophoresis is performed overnight.PCR-products that show mobility shifts are reamplified and sequenced toidentify nucleotide variation.

In a method called CGAP-GAI (DEMIGLACE), sequence and alignment data(from a PHRAP.ace file), quality scores for the sequence base calls(from PHRED quality files), distance information (from PHYLIP dnadistand neighbour programs) and base-calling data (from PHRED ‘-d’ switch)are loaded into memory. Sequences are aligned and examined for eachvertical chunk (‘slice’) of the resulting assembly for disagreement. Anysuch slice is considered a candidate SNP (DEMIGLACE). A number offilters are used by DEMIGLACE to eliminate slices that are not likely torepresent true polymorphisms. These include filters that: (i) excludesequences in any given slice from SNP consideration where neighboringsequence quality scores drop 40% or more; (ii) exclude calls in whichpeak amplitude is below the fifteenth percentile of all base calls forthat nucleotide type; (iii) disqualify regions of a sequence having ahigh number of disagreements with the consensus from participating inSNP calculations; (iv) removed from consideration any base call with analternative call in which the peak takes up 25% or more of the area ofthe called peak; (v) exclude variations that occur in only one readdirection. PHRED quality scores were converted into probability-of-errorvalues for each nucleotide in the slice. Standard Baysian methods areused to calculate the posterior probability that there is evidence ofnucleotide heterogeneity at a given location.

In a method called CU-RDF (RESEQ), PCR amplification is performed fromDNA isolated from blood using specific primers for each SNP, and aftertypical cleanup protocols to remove unused primers and free nucleotides,direct sequencing using the same or nested primers.

In a method called DEBNICK (METHOD-B), a comparative analysis ofclustered EST sequences is performed and confirmed by fluorescent-basedDNA sequencing. In a related method, called DEBNICK (METHOD-C),comparative analysis of clustered EST sequences with phred quality >20at the site of the mismatch, average phred quality >=20 over 5 bases5′-FLANK and 3′ to the SNP, no mismatches in 5 bases 5′ and 3′ to theSNP, at least two occurrences of each allele is performed and confirmedby examining traces.

In a method identified by ERO (RESEQ), new primers sets are designed forelectronically published STSs and used to amplify DNA from 10 differentmouse strains. The amplification product from each strain is then gelpurified and sequenced using a standard dideoxy, cycle sequencingtechnique with ³³P-labeled terminators. All the ddATP terminatedreactions are then loaded in adjacent lanes of a sequencing gel followedby all of the ddGTP reactions and so on. SNPs are identified by visuallyscanning the radiographs.

In another method identified as ERO (RESEQ-HT), new primers sets aredesigned for electronically published murine DNA sequences and used toamplify DNA from 10 different mouse strains. The amplification productfrom each strain is prepared for sequencing by treating with ExonucleaseI and Shrimp Alkaline Phosphatase. Sequencing is performed using ABIPrism Big Dye Terminator Ready Reaction Kit (Perkin-Elmer) and sequencesamples are run on the 3700 DNA Analyzer (96 Capillary Sequencer).

FGU-CBT (SCA2-SNP) identifies a method where the region containing theSNP were PCR amplified using the primers SCA2-FP3 and SCA2-RP3.Approximately 100 ng of genomic DNA is amplified in a 50 ml reactionvolume containing a final concentration of 5 mM Tris, 25 mM KCl, 0.75 mMMgCl₂, 0.05% gelatin, 20 pmol of each primer and 0.5 U of Taq DNApolymerase. Samples are denatured, annealed and extended and the PCRproduct is purified from a band cut out of the agarose gel using, forexample, the QIAquick gel extraction kit (Qiagen) and is sequenced usingdye terminator chemistry on an ABI Prism 377 automated DNA sequencerwith the PCR primers.

In a method identified as JBLACK (SEQ/RESTRICT), two independent PCRreactions are performed with genomic DNA. Products from the firstreaction are analyzed by sequencing, indicating a unique FspIrestriction site. The mutation is confirmed in the product of the secondPCR reaction by digesting with Fsp I.

In a method described as KWOK(1), SNPs are identified by comparing highquality genomic sequence data from four randomly chosen individuals bydirect DNA sequencing of PCR products with dye-terminator chemistry (seeKwok et al., 1996). In a related method identified as KWOK(2) SNPs areidentified by comparing high quality genomic sequence data fromoverlapping large-insert clones such as bacterial artificial chromosomes(BACs) or P1-based artificial chromosomes (PACs). An STS containing thisSNP is then developed and the existence of the SNP in variouspopulations is confirmed by pooled DNA sequencing (see Taillon-Miller etal., 1998). In another similar method called KWOK(3), SNPs areidentified by comparing high quality genomic sequence data fromoverlapping large-insert clones BACs or PACs. The SNPs found by thisapproach represent DNA sequence variations between the two donorchromosomes but the allele frequencies in the general population havenot yet been determined. In method KWOK(5), SNPs are identified bycomparing high quality genomic sequence data from a homozygous DNAsample and one or more pooled DNA samples by direct DNA sequencing ofPCR products with dye-terminator chemistry. The STSs used are developedfrom sequence data found in publicly available databases. Specifically,these STSs are amplified by PCR against a complete hydatidiform mole(CHM) that has been shown to be homozygous at all loci and a pool of DNAsamples from 80 CEPH parents (see Kwok et al., 1994).

In another such method, KWOK (OverlapSnpDetectionWithPolyBayes), SNPsare discovered by automated computer analysis of overlapping regions oflarge-insert human genomic clone sequences. For data acquisition, clonesequences are obtained directly from large-scale sequencing centers.This is necessary because base quality sequences are notpresent/available through GenBank. Raw data processing involves analyzedof clone sequences and accompanying base quality information forconsistency. Finished (‘base perfect’, error rate lower than 1 in 10,000bp) sequences with no associated base quality sequences are assigned auniform base quality value of 40 (1 in 10,000 bp error rate). Draftsequences without base quality values are rejected. Processed sequencesare entered into a local database. A version of each sequence with knownhuman repeats masked is also stored. Repeat masking is performed withthe program “MASKERAID.” Overlap detection: Putative overlaps aredetected with the program “WUBLAST.” Several filtering steps followed inorder to eliminate false overlap detection results, i.e. similaritiesbetween a pair of clone sequences that arise due to sequence duplicationas opposed to true overlap. Total length of overlap, overall percentsimilarity, number of sequence differences between nucleotides with highbase quality value “high-quality mismatches.” Results are also comparedto results of restriction fragment mapping of genomic clones atWashington University Genome Sequencing Center, finisher's reports onoverlaps, and results of the sequence contig building effort at theNCBI. SNP detection: Overlapping pairs of clone sequence are analyzedfor candidate SNP sites with the ‘POLYBAYES’ SNP detection software.Sequence differences between the pair of sequences are scored for theprobability of representing true sequence variation as opposed tosequencing error. This process requires the presence of base qualityvalues for both sequences. High-scoring candidates are extracted. Thesearch is restricted to substitution-type single base pair variations.Confidence score of candidate SNP is computed by the POLYBAYES software.

In method identified by KWOK (TaqMan assay), the TaqMan assay is used todetermine genotypes for 90 random individuals. In method identified byKYUGEN(Q1), DNA samples of indicated populations are pooled and analyzedby PLACE-SSCP. Peak heights of each allele in the pooled analysis arecorrected by those in a heterozygote, and are subsequently used forcalculation of allele frequencies. Allele frequencies higher than 10%are reliably quantified by this method. Allele frequency=0 (zero) meansthat the allele was found among individuals, but the corresponding peakis not seen in the examination of pool. Allele frequency=0-0.1 indicatesthat minor alleles are detected in the pool but the peaks are too low toreliably quantify.

In yet another method identified as KYUGEN (Method1), PCR products arepost-labeled with fluorescent dyes and analyzed by an automatedcapillary electrophoresis system under SSCP conditions (PLACE-SSCP).Four or more individual DNAs are analyzed with or without two pooled DNA(Japanese pool and CEPH parents pool) in a series of experiments.Alleles are identified by visual inspection. Individual DNAs withdifferent genotypes are sequenced and SNPs identified. Allelefrequencies are estimated from peak heights in the pooled samples aftercorrection of signal bias using peak heights in heterozygotes. For thePCR primers are tagged to have 5′-ATT or 5′-GTT at their ends forpost-labeling of both strands. Samples of DNA (10 ng/ul) are amplifiedin reaction mixtures containing the buffer (10 mM Tris-HCl, pH 8.3 or9.3, 50 mM KCl, 2.0 mM MgCl₂), 0.25 μM of each primer, 20004 of eachdNTP, and 0.025 units/μ1 of Taq DNA polymerase premixed with anti-Taqantibody. The two strands of PCR products are differentially labeledwith nucleotides modified with R110 and R6G by an exchange reaction ofKlenow fragment of DNA polymerase I. The reaction is stopped by addingEDTA, and unincorporated nucleotides are dephosphorylated by adding calfintestinal alkaline phosphatase. For the SSCP: an aliquot offluorescently labeled PCR products and TAMRA-labeled internal markersare added to deionized formamide, and denatured. Electrophoresis isperformed in a capillary using an ABI Prism 310 Genetic Analyzer.Genescan softwares (P-E Biosystems) are used for data collection anddata processing. DNA of individuals (two to eleven) including those whoshowed different genotypes on SSCP are subjected for direct sequencingusing big-dye terminator chemistry, on ABI Prism 310 sequencers.Multiple sequence trace files obtained from ABI Prism 310 are processedand aligned by Phred/Phrap and viewed using Consed viewer. SNPs areidentified by PolyPhred software and visual inspection.

In yet another method identified as KYUGEN (Method 2), individuals withdifferent genotypes are searched by denaturing HPLC (DHPLC) orPLACE-SSCP (Inazuka et al., 1997) and their sequences are determined toidentify SNPs. PCR is performed with primers tagged with 5′-ATT or5′-GTT at their ends for post-labeling of both strands. DHPLC analysisis carried out using the WAVE DNA fragment analysis system(Transgenomic). PCR products are injected into DNASep column, andseparated under the conditions determined using WAVEMaker program(Transgenomic). The two strands of PCR products that are differentiallylabeled with nucleotides modified with R110 and R6G by an exchangereaction of Klenow fragment of DNA polymerase I. The reaction is stoppedby adding EDTA, and unincorporated nucleotides are dephosphorylated byadding calf intestinal alkaline phosphatase. SSCP followed byelectrophoresis is performed in a capillary using an ABI Prism 310Genetic Analyzer. Genescan softwares (P-E Biosystems). DNA ofindividuals including those who showed different genotypes on DHPLC orSSCP are subjected for direct sequencing using big-dye terminatorchemistry, on ABI Prism 310 sequencer. Multiple sequence trace filesobtained from ABI Prism 310 are processed and aligned by Phred/Phrap andviewed using Consed viewer. SNPs are identified by PolyPhred softwareand visual inspection. Trace chromatogram data of EST sequences inUnigene are processed with PHRED. To identify likely SNPs, single basemismatches are reported from multiple sequence alignments produced bythe programs PHRAP, BRO and POA for each Unigene cluster. BRO correctedpossible misreported EST orientations, while POA identified and analyzednon-linear alignment structures indicative of gene mixing/chimeras thatmight produce spurious SNPs. Bayesian inference is used to weighevidence for true polymorphism versus sequencing error, misalignment orambiguity, misclustering or chimeric EST sequences, assessing data suchas raw chromatogram height, sharpness, overlap and spacing; sequencingerror rates; context-sensitivity; cDNA library origin, etc.

IX. PHARMACEUTICAL FORMULATIONS AND ROUTES OF ADMINISTRATION

The therapeutic compounds of the present disclosure may be administeredby a variety of methods, e.g., orally or by injection (e.g.subcutaneous, intravenous, intraperitoneal, etc.). Depending on theroute of administration, the active compounds may be coated in amaterial to protect the compound from the action of acids and othernatural conditions which may inactivate the compound. They may also beadministered by continuous perfusion/infusion of a disease or woundsite.

To administer the therapeutic compound by other than parenteraladministration, it may be necessary to coat the compound with, orco-administer the compound with, a material to prevent its inactivation.For example, the therapeutic compound may be administered to a patientin an appropriate carrier, for example, liposomes, or a diluent.Pharmaceutically acceptable diluents include saline and aqueous buffersolutions. Liposomes include water-in-oil-in-water CGF emulsions as wellas conventional liposomes (Strejan et al., 1984).

The therapeutic compound may also be administered parenterally,intraperitoneally, intraspinally, or intracerebrally. Dispersions can beprepared in glycerol, liquid polyethylene glycols, and mixtures thereofand in oils. Under ordinary conditions of storage and use, thesepreparations may contain a preservative to prevent the growth ofmicroorganisms.

Pharmaceutical compositions suitable for injectable use include sterileaqueous solutions (where water soluble) or dispersions and sterilepowders for the extemporaneous preparation of sterile injectablesolutions or dispersion. In all cases, the composition must be sterileand must be fluid to the extent that easy syringability exists. It mustbe stable under the conditions of manufacture and storage and must bepreserved against the contaminating action of microorganisms such asbacteria and fungi. The carrier can be a solvent or dispersion mediumcontaining, for example, water, ethanol, polyol (such as, glycerol,propylene glycol, and liquid polyethylene glycol, and the like),suitable mixtures thereof, and vegetable oils. The proper fluidity canbe maintained, for example, by the use of a coating such as lecithin, bythe maintenance of the required particle size in the case of dispersionand by the use of surfactants. Prevention of the action ofmicroorganisms can be achieved by various antibacterial and antifungalagents, for example, parabens, chlorobutanol, phenol, ascorbic acid,thimerosal, and the like. In many cases, it will be preferable toinclude isotonic agents, for example, sugars, sodium chloride, orpolyalcohols such as mannitol and sorbitol, in the composition.Prolonged absorption of the injectable compositions can be brought aboutby including in the composition an agent which delays absorption, forexample, aluminum monostearate or gelatin.

Sterile injectable solutions can be prepared by incorporating thetherapeutic compound in the required amount in an appropriate solventwith one or a combination of ingredients enumerated above, as required,followed by filtered sterilization. Generally, dispersions are preparedby incorporating the therapeutic compound into a sterile carrier whichcontains a basic dispersion medium and the required other ingredientsfrom those enumerated above. In the case of sterile powders for thepreparation of sterile injectable solutions, the preferred methods ofpreparation are vacuum drying and freeze-drying which yields a powder ofthe active ingredient (i.e., the therapeutic compound) plus anyadditional desired ingredient from a previously sterile-filteredsolution thereof.

The therapeutic compound can be orally administered, for example, withan inert diluent or an assimilable edible carrier. The therapeuticcompound and other ingredients may also be enclosed in a hard or softshell gelatin capsule, compressed into tablets, or incorporated directlyinto the subject's diet. For oral therapeutic administration, thetherapeutic compound may be incorporated with excipients and used in theform of ingestible tablets, buccal tablets, troches, capsules, elixirs,suspensions, syrups, wafers, and the like. The percentage of thetherapeutic compound in the compositions and preparations may, ofcourse, be varied. The amount of the therapeutic compound in suchtherapeutically useful compositions is such that a suitable dosage willbe obtained.

It is especially advantageous to formulate parenteral compositions indosage unit form for ease of administration and uniformity of dosage.Dosage unit form as used herein refers to physically discrete unitssuited as unitary dosages for the subjects to be treated; each unitcontaining a predetermined quantity of therapeutic compound calculatedto produce the desired therapeutic effect in association with therequired pharmaceutical carrier. The specification for the dosage unitforms of the invention are dictated by and directly dependent on (a) theunique characteristics of the therapeutic compound and the particulartherapeutic effect to be achieved, and (b) the limitations inherent inthe art of compounding such a therapeutic compound for the treatment ofa selected condition in a patient.

The therapeutic compound may also be administered topically to the skin,eye, or mucosa. Alternatively, if local delivery to the lungs is desiredthe therapeutic compound may be administered by inhalation in adry-powder or aerosol formulation.

Active compounds are administered at a therapeutically effective dosagesufficient to treat a condition associated with a condition in apatient. For example, the efficacy of a compound can be evaluated in ananimal model system that may be predictive of efficacy in treating thedisease in humans, such as the model systems shown in the examples anddrawings.

The actual dosage amount of a compound of the present disclosure orcomposition comprising a compound of the present disclosure administeredto a subject may be determined by physical and physiological factorssuch as age, sex, body weight, severity of condition, the type ofdisease being treated, previous or concurrent therapeutic interventions,idiopathy of the subject and on the route of administration. Thesefactors may be determined by a skilled artisan. The practitionerresponsible for administration will typically determine theconcentration of active ingredient(s) in a composition and appropriatedose(s) for the individual subject. The dosage may be adjusted by theindividual physician in the event of any complication.

An effective amount typically will vary from about 0.001 mg/kg to about1000 mg/kg, from about 0.01 mg/kg to about 750 mg/kg, from about 100mg/kg to about 500 mg/kg, from about 1.0 mg/kg to about 250 mg/kg, fromabout 10.0 mg/kg to about 150 mg/kg in one or more dose administrationsdaily, for one or several days (depending of course of the mode ofadministration and the factors discussed above). Other suitable doseranges include 1 mg to 10000 mg per day, 100 mg to 10000 mg per day, 500mg to 10000 mg per day, and 500 mg to 1000 mg per day. In someparticular embodiments, the amount is less than 10,000 mg per day with arange of 750 mg to 9000 mg per day. The effective amount may be lessthan 1 mg/kg/day, less than 500 mg/kg/day, less than 250 mg/kg/day, lessthan 100 mg/kg/day, less than 50 mg/kg/day, less than 25 mg/kg/day orless than 10 mg/kg/day. It may alternatively be in the range of 1mg/kg/day to 200 mg/kg/day. For example, regarding treatment of diabeticpatients, the unit dosage may be an amount that reduces blood glucose byat least 40% as compared to an untreated subject. In another embodiment,the unit dosage is an amount that reduces blood glucose to a level thatis ±10% of the blood glucose level of a non-diabetic subject.

In other non-limiting examples, a dose may also comprise from about 1micro-gram/kg/body weight, about 5 microgram/kg/body weight, about 10microgram/kg/body weight, about 50 microgram/kg/body weight, about 100microgram/kg/body weight, about 200 microgram/kg/body weight, about 350microgram/kg/body weight, about 500 microgram/kg/body weight, about 1milligram/kg/body weight, about 5 milli-gram/kg/body weight, about 10milligram/kg/body weight, about 50 milligram/kg/body weight, about 100milligram/kg/body weight, about 200 milligram/kg/body weight, about 350milligram/kg/body weight, about 500 milligram/kg/body weight, to about1000 mg/kg/body weight or more per administration, and any rangederivable therein. In non-limiting examples of a derivable range fromthe numbers listed herein, a range of about 5 mg/kg/body weight to about100 mg/kg/body weight, about 5 microgram/kg/body weight to about 500milligram/kg/body weight, etc., can be administered, based on thenumbers described above.

In certain embodiments, a pharmaceutical composition of the presentdisclosure may comprise, for example, at least about 0.1% of a compoundof the present disclosure. In other embodiments, the compound of thepresent disclosure may comprise between about 2% to about 75% of theweight of the unit, or between about 25% to about 60%, for example, andany range derivable therein.

Single or multiple doses of the agents are contemplated. Desired timeintervals for delivery of multiple doses can be determined by one ofordinary skill in the art employing no more than routineexperimentation. As an example, subjects may be administered two dosesdaily at approximately 12 hour intervals. In some embodiments, the agentis administered once a day.

The agent(s) may be administered on a routine schedule. As used herein aroutine schedule refers to a predetermined designated period of time.The routine schedule may encompass periods of time which are identicalor which differ in length, as long as the schedule is predetermined. Forinstance, the routine schedule may involve administration twice a day,every day, every two days, every three days, every four days, every fivedays, every six days, a weekly basis, a monthly basis or any set numberof days or weeks there-between. Alternatively, the predetermined routineschedule may involve administration on a twice daily basis for the firstweek, followed by a daily basis for several months, etc. In otherembodiments, the invention provides that the agent(s) may taken orallyand that the timing of which is or is not dependent upon food intake.Thus, for example, the agent can be taken every morning and/or everyevening, regardless of when the subject has eaten or will eat.

X. COMBINATION THERAPY

Effective combination therapy may be achieved with a single compositionor pharmacological formulation that includes both agents, or with twodistinct compositions or formulations, administered at the same time,wherein one composition includes a compound of this invention, and theother includes the second agent(s). Alternatively, the therapy mayprecede or follow the other agent treatment by intervals ranging fromminutes to months.

Various combinations may be employed, such as where “A” represents thefirst agent (e.g., DFMO) and “B” represents a secondary agent (e.g.,sulindac), non-limiting examples of which are described below:

A/B/A B/A/B B/B/A A/A/B A/B/B B/A/A A/B/B/B B/A/B/B B/B/B/A B/B/A/BA/A/B/B A/B/A/B A/B/B/A B/B/A/A B/A/B/A B/A/A/B A/A/A/B B/A/A/A A/B/A/AA/A/B/A

XI. EXAMPLES

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples which follow representtechniques discovered by the inventor to function well in the practiceof the invention, and thus can be considered to constitute preferredmodes for its practice. However, those of skill in the art should, inlight of the present disclosure, appreciate that many changes can bemade in the specific embodiments which are disclosed and still obtain alike or similar result without departing from the spirit and scope ofthe invention.

Example 1—Epidemiologic Studies: ODC +316 SNP Associations withCRC-Specific Survival

Experimental Design:

The study included 440 incident CRC cases from the population-based UCIrvine Gene-Environment Study of Familial CRC (diagnosed 1994-1996 withfollow-up through March 2008). The primary outcome was CRC-specificsurvival (CRC-SS) dependent on ODC genotype (GG vs. AA/GA). In humancolon cancer cell lines, ODC allele-specific binding of E-boxtranscription factors was determined via western blotting and chromatinimmunoprecipitation (CHIP) assays. ODC allele-specific promoter activitywas determined using promoter constructs in combination with vectorsexpressing either the transcriptional activator c-MYC or the repressorMAD1.

Results:

Genotype-specific survival differences among CRC cases were limited tocolon cancer cases: compared to ODC GG genotype cases (HR=1.00,reference) the adjusted CRC-SS hazards ratio (HR) was 2.31 (1.15-4.64)for ODC GA cases and 3.73 (0.93-14.99) for ODC AA cases (P-trend=0.006).In colon cancer cells, the ODC +316 SNP, flanked by two E-boxes,predicts ODC promoter activity. The E-box activator −MYC and repressorsMAD1 and MAD4 preferentially bind to minor A−, compared to major G−,alleles in cultured cells.

Study Population.

We studied incident cases of invasive CRC enrolled in the University ofCalifornia, Irvine Gene-Environment Study of Familial Colorectal Cancer(Peel et al., 2000; Zell et al., 2007) during 1994-1996 with follow-upthrough March 2008. The parent study was designed to determine theincidence of HNPCC in a large, population-based cohort of colorectalcancer cases. Participants were identified through the population-basedcancer registries of the Cancer Surveillance Program of OrangeCounty/San Diego Imperial Organization for Cancer Control using theApril 2008 data file. In the parent study (Peel et al., 2000), allsubjects with CRC diagnosed at all ages in Orange County, Calif., from1994 to 1996 were ascertained. All subjects diagnosed in San Diego andImperial Counties, Calif., at ages <65 y between 1994 and 1995 were alsoascertained. Cases were then contacted if they were eligible for thestudy (alive at the time ascertained and having a contact address) andif their physicians did not deny permission to contact. At the time ofstudy entry, cases signed a consent form allowing for blood draws andthe release of medical information. This study was approved by the UCIrvine Institutional Review Board (#93-257). Clinical and demographicdata including vital status and follow-up were obtained through linkageto the regional cancer registry databases as previously described (Peelet al., 2000; Zell et al., 2007; Zell et al., 2008). Tumor, node,metastasis (TNM) staging determination was derived from existing AJCCcodes where available and conversion of extent of disease codes, aspreviously reported (Le et al., 2008). Family history of cancer in afirst-degree relative was ascertained by self-reporting during atelephone interview conducted at enrollment (Zell et al., 2008; Ziogasand Anton-Culver, 2003). Twenty-two cases with hereditary non-polyposiscolon cancer (HNPCC), as defined by Amsterdam criteria, were identifiedand excluded from the analysis. The median time from CRC diagnosis untilstudy entry (i.e., date of family history interview) was 16 months (95%CI 12-23 months).

DNA Extraction and ODC +316 SNP Genotyping.

DNA was extracted from 2.0 mL red blood cell clot samples using theQIAGEN QIAamp DNA Midi or Mini Kits, (Qiagen) following themanufacturer's instructions. Genotyping of the ODC +316 SNP wasconducted using oligonucleotide primers designed to amplify a 172-bpfragment containing the polymorphic base at +316 (Applied Biosystems,Foster City, Calif.). Allele-specific TaqMan probes were synthesizedwith different 5′ labels (6-carboxyflourescein or VIC) and the same 3′quencher dye (6-carboxytetramethylrhodamine) (23). Each PCR reaction (5μL total) contained 10 ng of participant DNA, 30 pmol of each primer,12.5 pmol of each TaqMan probe, and 1×TaqMan Universal PCR Master Mix(Applied Biosystems, Foster City, Calif.), as previously reported(Martinez et al., 2003; Guo et al., 2000).

Statistical Analysis—Population-Based Study.

Sample size was determined based on an estimated 1:1 ratio of ODC GGgenotype to ODC GA/AA genotype (Martinez et al., 2003; Barry et al.2006; Hubner et al., 2008; Guo et al., 2000). Prior analysis of datafrom 1154 colon and rectal cancer cases in the UC IrvineGene-Environment Study of Familial CRC revealed that 10-yearCRC-specific survival approximated 66% (Zell et al., 2008). Theinventors proposed a 15% or greater difference in CRC-specific survivalbased on ODC genotype alone for our sample size calculations. Thus, 315total subjects were needed to detect the proposed difference in 10-yearCRC-specific survival between two groups at 5% significance level with80% power: 55% in group 1 vs. 70% in group 2. 440 of 481 DNA sampleswere successfully genotyped. 41 cases (8.5%) resulted in an undeterminedODC +316 genotype due to low DNA concentration and/or poor DNA quality,however no clinicopathologic differences were observed between thesuccessfully genotyped and unsuccessfully genotyped cases. Thus thestudy was sufficiently powered to address the primary endpoint.

Comparisons of demographic, clinical, and pathologic variables amongcolon and rectal cases were done using Pearson chi-square statistic orFisher's exact test for nominal variables and Student t-test forcontinuous variables. Colorectal cancer-specific survival was defined asmortality from CRC itself, and data censoring occurred in the followinginstances: alive at the end of follow-up, loss to follow-up, or deathfrom any cause other than CRC. Overall survival (OS) was defined withmortality from any cause. Survival curves were constructed for colon andrectal cancer cases using the Kaplan-Meier method and analyzed with thelog rank test for univariate analyses. Cox proportional hazards modelingwas performed for all CRC cases, colon cancer cases, and rectal cancercases using time since diagnosis to profile the adjusted risk of overalland CRC-specific death based on ODC genotype. The effects of ODCgenotype (GG, GA, or AA) on survival were analyzed in the Cox modelswith adjustment for the following covariates: age, gender, ethnicity,family history of CRC, TNM stage at diagnosis, tumor site within thecolon, histologic subtype, treatment with surgery, radiation therapy,and chemotherapy. Each variable in the model was coded using dummyvariables. All analyses were conducted using SAS 9.2 statisticalsoftware (SAS Institute, Cary, N.C.). Statistical significance wasassumed for a 2-tailed P value <0.05.

Example 2—Experimental Studies: ODC +316 SNP Regulation in Colon CancerCells

Cell Culture.

The human colon cancer cell lines HT29 and HCT116 were maintained inMcCoy's 5A medium (Invitrogen, Carlsbad, Calif.). All media used weresupplemented with 10% FBS plus 1% penicillin/streptomycin solution(Invitrogen, Carlsbad, Calif.). Cultures were maintained at 37° C. in ahumidified atmosphere of 5% CO2.

Genotyping Assay.

DNA samples from HT29 and HCT116 cells were subjected to a PCR-RFLPprocedure to detect the polymorphic PstI site. Sequences were amplifiedby PCR, using the following primers: 5′-TCTGCGCTTCCCCATGGGGCT-3′ (SEQ IDNO:1) and 5′-TTTCCCAACCCTTCG-3′ (SEQ ID NO:2). Each reaction contained—1μl DNA, 4 pmol of each primer, 12.5 μl 2×PCR PreMixes buffer “G”(EPICENTRE Biotechnologies, Madison, Wis.) and 0.5 unit of Taq DNApolymerase, in a final volume of 25 μl. The expected size of the PCRproduct was 351 bp. After amplification, 10-20 μl of the PCR productwere digested with 10 units of PstI in 30 μl for 2 hours at 37° C. DNAfrom HT29 cells (GA), containing the PstI site, yielded two fragments of156 and 195 bp.

Western Blot Analysis.

Cells were harvested, lysed and proteins were separated on a 12.5%SDS-PAGE gel. Proteins were transferred by electrophoresis onto aHybond-C membrane. The membrane was blocked with Blotto A (5% blockinggrade dry milk in TTBS solution) and probed using 1:300 dilutions ofprimary antibodies (Santa Cruz Biotechnology, Santa Cruz, Calif.) inBlotto A. Primary antibodies were incubated at 4° C. overnight, followedby incubation with an appropriate HRP-tagged secondary antibody (1:1000dilution) for 1 hour at room temperature. Chemiluminescent detection wasconducted using ECL Western Detection reagent (Amersham Biosciences,Piscataway, N.J.) and exposed on Biomax XAR film (Kodak).

Chromatin Immunoprecipitation (CHIP).

CHIP assays were performed using a commercial kit, as recommended by themanufacturer (Upstate Biotech, Lake Placid, N.Y., USA). Briefly, cellswere treated with 1% formaldehyde to crosslink DNA and proteins, andDNA-protein complexes were disrupted by sonication to lengths between200 to 1000 bp. Lysates were diluted 10-fold with immunoprecipitation(IP) dilution buffer containing protease inhibitors. Antibodies forc-MYC, MAD1 and MAD4 (Santa Cruz Biotechnology, Santa Cruz, Calif.) wereused to precipitate chromatin, while additional sample was left as aminus-antibody (−Ab) control. Samples were immunoprecipitated overnightat 4° C. with rotation. Immune complexes were obtained by adding 60 ulof salmon sperm DNA/protein A Agarose slurry and incubating for an hourat 4° C. with rotation followed by gentle centrifugation (1000 rpm, 1min). Protein A agarose pellets were washed with low salt buffer, highsalt buffer, LiCl buffer and TE buffer. Then the complexes were elutedby adding 250 μl elution buffer (0.1M NaHCO₃, 1% SDS) twice, andDNA-protein crosslinks were reversed with 0.2 M NaCl by heating at 65°C. for 4 hours for all samples, including the input DNA and −Ab DNAcontrols. DNA was resuspended in 30 ul of ddH2O. For visualization ofPCR product and its size, standard PCR reactions were carried out. Thesequences of ODC primers used for PCR were 5′-CCTGGGCGCTCTGAGGT-3′ (SEQID NO:3) (17 mer) and 5′-AGGAAGCGGCGCCTCAA-3′ (SEQ ID NO:4) (17 mer).Quantitative real-time PCR was performed using TaqMan gene expressionassays kit (Applied Biosystems, Foster City, Calif.) on an ABI7700sequence detection system. Details for the computation of relativebinding can be found on the manufacturer's web site(http://www.appliedbiosystems.com/).

Transient Transfections.

Transient transfections were preformed using LipofectAMINE reagent(Invitrogen, Carlsbad, Calif.) according to the manufacturer's protocol,as detailed in the supplementary file. HCT116 and HT29 cells weretransfected with 1 μg of pGL3-ODC/A or pGL3-ODC/G plasmids (Martinez etal., 2003) along with 0.01 μg of Renilla-TK plasmid. The Renilla-TKplasmid was purchased from Promega (Madison, Wis.) and used as atransfection efficiency control in all promoter-reporter transfectionexperiments. For c-MYC experiments, ODC pGL3-plasmids wereco-transfected with either pcDNA 3.0 or CMV-c-MYC expression vector(OriGene, Rockville, Md.). For MAD1 experiments, the ODC plasmids wereco-transfected with either pcDNA 3.1 or pcDNA-MAD1. For c-MYC and MAD1co-transfection, ODC promoter reporter constructs were prepared whichcontain the first 1.6 Kb of the ODC gene cloned into a pGL3 vector. Theconstructs included E-box 1 (−485 to −480 bp) intact (wt E-box 1) ordeleted (mut E-box 1). Additionally, both variants of the +316 ODC SNPwere used, creating a total of 4 different constructs. After 6 hours ofincubation, cells were supplemented with complete medium containing 20%FBS and left to grow overnight. The next day after transfection 20%FBS-containing complete medium was replaced with 10% FBS-containingmedium. 48 hours after transfection, cells were washed with PBS andlysed in Passive Lysis Buffer from the Dual Luciferase Assay kit(Promega, Madison, Wis.). Dual luciferase activities were measured usinga Turner Designs TD-20/20 luminometer, as described by the manufacturer,and presented as relative luciferase units (RLU). Experiments werepreformed in triplicates and repeated at least 2 times.

Statistical Analysis—Experimental Studies.

For transient transfection experiments, two-sample t-tests were used(Microsoft Excel Microsoft Corp., Redmond, Wash.). The effect of c-MYCexpression on ODC allele-specific promoter activity was examined in HT29colon cancer cells using ODC promoter constructs differing by thepresence of the first E-box element: (a) wild type (wt) E-box1 +316 G,(b) mutant (mut) E-box1 +316 G, (c) wt E-box1 +316 A, and (d) mut E-box1+316 A. For each promoter construct, two-sample t-tests were used tocompare promoter activity between cells co-transfected with pcDNA3.0plasmid versus those transfected with the CMV-c-MYC expression vector.Similarly, to examine the effect of MAD1 expression on ODCallele-specific promoter activity, two-sample t-tests were used tocompare the effect of promoter activity in promoter constructsco-transfected with pcDNA3.1 plasmid versus those transfected withpcDNA-MAD1 plasmid. Statistical significance was assumed for a 2-tailedP value <0.05.

Example 3—Differential Affects of ODC1 Genotype

This study involves analysis of patient data from the multicenter phaseIII colon adenoma prevention trial (Meyskens et al., 2008). 375 patientswere enrolled, and the study was halted by the Data Safety MonitoringBoard (DSMB) after 267 patients completed end-of-study colonoscopies(due to the study meeting its efficacy endpoints). The DSMB monitoredall safety and efficacy endpoints. Blood specimens were collected on 228consenting study patients for genotyping analysis after November 2002(including 159 of 246 patients randomized before, and 69 of 129 patientsrandomized after this date), when the protocol was modified in light ofdata demonstrating the importance of the ODC1 SNP (2). ODC1 (rs2302615)genotyping was conducted on patient-derived genomic DNA usingallele-specific TaqMan probes as described previously (Guo et al.,2000). Rectal tissue polyamine content was determined as describedpreviously (Meyskens et al., 1998; Seiler and Knodgen, 1980), using 3 of8 randomly selected rectal mucosal biopsy specimens. Tissue polyamineresponse was performed for response values ranging from 25% to 45%.

ODC1 genotype was analyzed under a dominant model: AA/GA vs. GGpatients. Wilcoxon Rank Sums tests were performed on non-normallydistributed continuous variables across two genotype groups. Chi-squaretests or Fisher's Exact Test were utilized to assess the associationbetween baseline categorical variables and genotype group. Log binomialregression was performed on the primary outcome (adenoma recurrence)with predictors: treatment group, age, gender, race (Caucasian vs.other), aspirin usage, ODC1 genotype (in the dominant model), and a termrepresenting the treatment by genotype interaction. For secondaryoutcomes (rectal tissue polyamine response, toxicities), the effects oftreatment group, genotype, and interaction between treatment andgenotype were examined using full log binomial models. Statisticalanalyses were conducted using SAS 9.2 statistical software (SAS Inc.,Cary, N.C.). Patients signed informed consent for trial inclusion andspecimen retrieval/analysis. The study was approved after full committeereview by the UC Irvine institutional review board (IRB protocol#2002-2261) and review by each of the local IRBs at participating studysites.

ODC1 genotype distribution was: 126 GG (55%), 87 GA (38%), and 15 AA(7%). Baseline clinical characteristics revealed differences, as shownin Table 1. The relative risk (RR) for adenoma recurrence related totreatment after adjustment in the full regression model was 0.39 (95% CI0.24-0.66). Among patients receiving placebo or treatment, respectively,ototoxicity occurred in 23% vs. 22% of ODC1 GG patients, 20% vs. 21% ofODC1 GA patients, and 0% (0 of 7) vs. 57% (4 of 7) of ODC1 AA patients.

TABLE 1 Clinical Characteristics of all Subjects at Baseline (n = 228)by ODC1 Genotype. ODC1 AA/GA ODC1 GG genotype (n = 102) genotype (n =126) P* Mean Age (years ± Standard 60.2 ± 8.4 SD 62.6 ± 8.7 SD 0.024^(†)Deviation) Gender (n, %) Male 77 (75%) 96 (76%) 0.90 Female 25 (25%) 30(24%) Race (n, %) White 84 (82%) 107 (85%) 0.007^(‡) Black 3 (3%) 4 (3%)Hispanic 4 (4%) 12 (10%) Asian 9 (9%) 1 (1%) Other 2 (2%) 2 (2%)Treatment group (n, %) Eflornithine + sulindac 46 (45%) 71 (56%) 0.09Placebo 56 (55%) 55 (44%) Low-dose aspirin use (n, %) Yes 44 (43%) 54(43%) 0.97 No 58 (57%) 72 (57%) Median no. (with minimum-maximum) 2.00(1, 11) 2.00 (1, 16) 0.41^(†) Location of largest prior polyp (n, %)Rectum 26 (25%) 23 (18%) 0.19 Colon 76 (75%) 103 (82%) Prior polyphistology (n, %) Tubular 76 (75%) 99 (79%) 0.03^(‡) Adenoma-NOS 6 (6%) 8(6%) Tubulovillous 10 (10%) 17 (13%) Villous 7 (7%) 1 (1%) Carcinomain-situ 3 (3%) 0 (0%) Tubular adenoma, high-grade 0 (0%) 1 (1%)dysplasia Largest polyp ≥1 cm (n, %) 25 (25%) 40 (32%) 0.23 Treatmentrendered for prior polyp (n, 92 (90%) 117 (93%) 0.47 %) Completeendoscopic removal 10 (10%) 9 (7%) Surgery Baseline tissue polyaminecontent^(§) (median, nmol/mg protein, range) Putrescine 0.47 (0.01-4.60)0.56 (0.01-5.29) 0.48^(†) Spermidine 1.99 (0.76-9.18) 2.17 (1.05-8.97)0.08^(†) Spermine 6.82 (2.29-19.86) 7.29 (2.72-22.85) 0.23^(†)Spermidine:Spermine ratio 0.30 (0.19-0.98) 0.31 (0.19-0.76) 0.23^(†)*p-value for the χ² test is listed unless noted otherwise. ^(†)p-valuefor the Wilcoxon Rank Sums test. ^(‡)p-value for the Fisher Exact test.^(§)Tissue polyamine data missing for 1 subject with ODC1 GG genotypeand 1 subject with ODC1 AA/GA genotype

TABLE 2 Multivariate Overall Survival and Colorectal Cancer-SpecificSurvival Analysis for Colorectal Cancer Cases Based on ODC1 Genotype.ODC1 Genotype GG GA/AA P Overall mortality Number of events  47  62Number at risk 208 192 Unadjusted HR (95% CI) 1 (reference) 1.57(1.07-2.29) 0.020 Adjusted HR (95% CI)* 1 (reference) 1.58 (1.07-2.34)0.021 CRC-specific mortality Number of events  22  37 Number at risk 208192 Unadjusted HR (95% CI) 1 (reference) 1.97 (1.16-3.34) 0.012 AdjustedHR (95% CI)* 1 (reference) 2.02 (1.17-3.50) 0.012 Abbreviation: 95% CI,95% confidence interval. *Includes stratification for stage (I, II, III)and adjustment for age (y), gender, ethnicity, family history ofcolorectal cancer, TNM stage at diagnosis, tumor site within thecolorectum, histologic subtype, treatment with surgery, radiationtherapy, and chemotherapy.

TABLE 3 Incidence of Events after Randomization and Stratified by ODC1Genotype (Dominant Model). Eflornithine/ Placebo Sulindac (n = 111) (n =117) ODC1 GA ODC1 GA ODC1 GG or AA ODC1 GG or AA P* Any adenomarecurrence 22/44 (50) 18/53 (34)   7/64 (11) 9/42 (21) <0.0001 Anyadverse event - no. of patients with adverse events (%) Cardiovascularevents^(†)  8/55 (15) 8/56 (14) 13/71 (18) 9/46 (20) 0.30 no. ofpatients (%) Gastrointestinal events^(‡), 4/55 (7) 8/56 (14)  9/71 (13)7/46 (15) 0.54 no. of patients (%) Hearing loss at least 15 dB at ≥2frequencies, 10/44 (23) 9/52 (17) 14/63 (22) 11/41 (27)  0.26 no. ofpatients (%) *P-value for the likelihood ratio test for treatment effect(eflornithine and sulindac vs. placebo) on adenoma recurrence in thefull model which includes age, gender, race/ethnicity, aspirin usage,treatment, genotype, and treatment and genotype interaction ascovariates. A statistically significant interaction was detected in thefull model for adenoma recurrence (P = 0.038); no interaction wasdetected for cardiovascular toxicity, gastrointestinal toxicity, orototoxicity. ^(†)Cardiovascular events included coronary artery disease,myocardial infarction, cerebrovascular accident, congestive heartfailure, and chest pain. ^(‡)Gastrointestinal events includedgastrointestinal bleeding (from any region) such as rectal bleeding,upper gastrointestinal bleeding, hematochezia, or occult blood in thestool.

TABLE 4 Efficacy and Adverse Events and the ODC1 + 316 SNP. Placebo (N =111) DFMO/Sulindac (N = 117) ODC GG ODC GA ODC AA ODC GG ODC GA ODC AA(N = 55) (N = 48) (N = 8) (N = 71) (N = 39) (N = 7) P Any adenoma 22/44(50) (35) (29) 7/64 (11) (14) (57) <0.0001 recurrence (%) Cardiovascularevents 8/55 (15) 7/48 (15) 1/8 (13) 13/71 (18) 7/39 (18) 2/7 (29) 0.37no. of patients (%)a Gastrointestinal events 4/55 (7) 8/48 (17) 0/8 (0)9/71 (13) 5/39 (13) 2/7 (29) 0.45 no. of patients (%)b Hearing loss atleast 15 dB 10/44 (23) 9/45 (20) 0/8 (0) 14/63 (22) 7/34 (21) 4/7 (57)0.020 at ≥2 frequencies, no. of patients (%)c

All of the methods disclosed and claimed herein can be made and executedwithout undue experimentation in light of the present disclosure. Whilethe methods of this invention have been described in terms of preferredembodiments, it will be apparent to those of skill in the art thatvariations may be applied to the methods and in the steps or in thesequence of steps of the method described herein without departing fromthe concept, spirit and scope of the invention. More specifically, itwill be apparent that certain agents which are both chemically andphysiologically related may be substituted for the agents describedherein while the same or similar results would be achieved. All suchsimilar substitutes and modifications apparent to those skilled in theart are deemed to be within the spirit, scope and concept of theinvention as defined by the appended claims.

REFERENCES

The following references to the extent that they provide exemplaryprocedural or other details supplementary to those set forth herein, arespecifically incorporated herein by reference.

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1-121. (canceled)
 122. A method for treating a patient with carcinoma,the method comprising administering to a patient with carcinoma acombination therapy comprising a combined effective amount of anornithine decarboxylase (ODC) inhibitor and an agent that modulates thepolyamine pathway to reduce overall cellular polyamine content, saidpatient having been determined to have a dietary polyamine intake thatis 300 μmol polyamine per day or lower.
 123. The method of claim 122,wherein said patient has been further determined to have a G atrs2302615 (position +316) of at least one allele of the ODC1 genepromoter.
 124. The method of claim 123, wherein said patient has beenfurther determined to have a genotype of GG at rs2302615 of both allelesof the ODC1 gene promoter.
 125. The method of claim 123, wherein saidpatient has been further determined to have a genotype of GA atrs2302615 of both alleles of the ODC1 gene promoter.
 126. The method ofclaim 123, wherein the method prevents ototoxicity or the risk thereofwithin the patient.
 127. The method of claim 122, wherein said ornithinedecarboxylase (ODC) inhibitor is α-difluoromethylornithine (DFMO). 128.The method of claim 122, wherein the agent that modulates the polyaminepathway to reduce overall cellular polyamine content is aspermidine/spermine N¹-acetyltransferase expression agonist.
 129. Themethod of claim 128, wherein said spermidine/spermineN¹-acetyltransferase expression agonist is a non-aspirin containingnon-steroidal anti-inflammatory drug (NSAID).
 130. The method of claim129, wherein said non-aspirin containing NSAID is a selective COX-2inhibitor.
 131. The method of claim 130, wherein said non-aspirincontaining NSAID is sulindac.
 132. The method of claim 122, wherein saiddietary polyamine intake is determined from a patient dietary history.133. The method of claim 122, wherein said patient has a solid tumor,and said method further comprises resection of said solid tumor. 134.The method of claim 132, wherein DFMO and sulindac are administeredprior to said resection.
 135. The method of claim 132, wherein DFMO andsulindac are administered after said resection.
 136. The method of claim122, wherein the carcinoma is colorectal cancer, breast cancer,pancreatic cancer, brain cancer, lung cancer, stomach cancer, a bloodcancer, skin cancer, testicular cancer, prostate cancer, ovarian cancer,liver cancer or esophageal cancer, cervical cancer, head and neckcancer, non-melanoma skin cancer, neuroblastoma, or glioblastoma. 137.The method of claim 136, wherein the carcinoma is colorectal cancer.138. The method of claim 137, wherein the colorectal cancer isassociated with familial adenomatous polyposis.
 139. The method of claim122, wherein the patient is a human.
 140. A method for preventingrecurrence in a patient previously diagnosed with carcinoma, the methodcomprising administering to a patient previously diagnosed withcarcinoma a combined effective amount of an ornithine decarboxylase(ODC) inhibitor and a spermidine/spermine N¹-acetyltransferaseexpression agonist, said patient having been determined to have adietary polyamine intake that is 300 μmol polyamine per day or lower.141. A method for preventing carcinoma in a patient having a familialhistory of carcinoma, the method comprising administering to a patienthaving a familial history of carcinoma a combined effective amount of anornithine decarboxylase (ODC) inhibitor and a spermidine/spermineN¹-acetyltransferase expression agonist, said patient having beendetermined to have a dietary polyamine intake that is 300 μmol polyamineper day or lower.